Incompatible Ligand-Residue Pairs in LacI Family of Transcription
Factors
Yuriy Korostelev
Institute for Information Transmission Problems
[email protected]
Matvei Khoroshkin
Institute for Information Transmission Problems
[email protected]
Mikhail S. Gelfand
Institute for Information Transmission Problems
[email protected]
from binding to promotor on DNA. Thus mechanisms
providing ligand-specicity play an important role
in gene regulation. Better understanding of such
mechanisms can allow one to exploit transcription
factors in genetic engeneering experiments.
LacI transcription factors bind dozens of various
ligands. Here we employ a statistical approach to
identify LacI protein positions which correlate with the
ligand. We further analyse contacts of such positions
with the ligands in various crystal structures of LacIfamily member with the ligand.
Àííîòàöèÿ
We studied protein-ligand recognition in the LacI
family of transcription factors. We identied protein
positions responsible for specic sugar recognition
(specicity determining positions, SDP) using sequence
data. We compared identied SDPs with 3D structure
data and obtained further evidence of importance
of these positioins. Ligand-contacting positions list
was compared with SDPs. The majority of positions
consistently contacting with the ligand appeared to be
SDPs. Eight available 3D structures of complexes of
LacI-familey proteins bound to dierent sugars were
superimposed to identify SDP-ligand pairs that are
incompatible. We specically studied the best specicity
determining position 115. Structural analysis revealed
the Gly115 → Asp115 substitution to interfere with
disaccharide binding. Thus bulky Asp115 favors small
monosacharides in the binding center, while Gly115
allows binding of dissacharides.
2. Methods
LacI transcription factors and their ligands data
were obtained from comparative genomics study
paper[?]. Specicity determining positions (SDP) were
identied via SDPpred[?]. Eight crystal structures were
obtained from Protein Data Bank[1] (ids: 3CTP, 3K4H,
2GX6, 2P9H, 1BYK, 2NZU, 3TB6, 3O75). Residueligand contacts were identied in pymol[4] with 3.5
angstrom threshold. Ligand binding domains were
superimposed in Swiss-PdbViewer[3] by aligned α helixes regions.
1. Introduction
LacI family transcription factors usually sense
sugar eectors and regulate carbohydrate utilization
genes. The protein consists of DNA-binding domain
(usually helix-turn-helix) and ligand binding domain.
The later is homologus to the periplasmic proteins of
ABC-transporters[2].
Binding of ligand induces allosteric conformational
changes of the ligand binding domain which further
leads to changes in the DNA-binding domain which
ultimately either allows or prevents transcription factor
3. Results
Based on the ligand transcription factors were
divided into 31 specicity groups. 15 protein positions
appeared to be correlated with the ligand (SDP
positions). From them seven appear to have contacts
with ligand in seven or all eight structures. Two
more positions have contacts in four structures.
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regulons of the laci-family transcription factors. Front
Microbiol, 5:294, 2014.
[6] Schr
odinger, LLC. The PyMOL molecular graphics
system, version 1.8. November 2015.
Three residues appeared to be contacting with the
ligand in two structures but were not correlated
with ligand. Overall all positions with contacts in
four or more structures appeared to be correlated.
Thus substitutions in residues that are consistently
contacting with ligand are likely to aect ligand
specicity.
We tried to identify incompatible residue-ligand
pairs in studied structures. For that we superimposed
ligand-binding domains and asumed that 'alien' ligands
would bind protein as in their native counterpart. We
closely analysed the best correlated SDP 115. In 3K4H
structure transcription factor has Gly115 and is bound
to maltose while in for example 2GX6 a more common
Asn115 is present and Ribose is bound. Superimposition
of these two structures shows that disaccharide maltose
is sterically incompatible with Asn115 or any other long
residue. We substituted Gly115 for Asn115 in 3K4H
structure and with all other residues frosen performed
structure energy optimisation (simulated annealing
option in Swiss-PdbViever). It turns out Asn115 can
not adopt proper conformation with maltose being
too close to backbone. These nding suggest Gly115
may be a simple option for the transcription factor to
accomodate large sugars.
4. References
Ñïèñîê ëèòåðàòóðû
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Parallel evolution of ligand specicity
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Feb 2003.
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32(Web Server issue):W424W428, Jul 2004.
[5] Dmitry A. Ravcheev, Matvei S. Khoroshkin, Olga N.
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