Computational design of protein function Loren Looger Hellinga lab
Jan 08, 2016
Computational design of protein function
Loren Looger
Hellinga lab
1. Allowable structures for proteins, DNA, small molecules
Progesterone
2. Pseudo-geometric potential
H-bonds
electrostatics
sterics
solvation
Pretty much like CHARMM...
E
r
E=Ar12 −
Br6
E'(r)=E(rmin −rmin −rα
),r <rmin
~ 1.1
Hydrogen bonds, too...
D
HA
anchorr
5roptr
⎛
⎝ ⎜
⎞
⎠ ⎟
12
−6roptr
⎛
⎝ ⎜
⎞
⎠ ⎟
10
cos2θ cos2 φopt−φ( )-8 · { } · ·
Area-based solvation energy
P P
H H
H
P = polarH = hydrophobic
Electrostatic potential
€
E =q1q2
εr
is a function of atom-type pair &protein environment.
Parameterized to fit experimental data.
3. Algorithm for choosing best structure(s) from all available
Complementary Surface Construction:Complementary Surface Construction:
Molten zone
Evolving zone
Fixed zone
Ligandcoordinates
Proteincoordinates
Poly-alaninePCS
Rotationalligand
ensembleDocking
grid
Force field
Placedligand
ensemble
Fixed ligand ensemble
Side-chainrotamers
EvolvedPCS
ensemble
Ranked PCS ensemble
Experiments
Periplasmic Binding Protein (PBP) scaffolds
MetabolitesMetabolites
ExplosivesExplosives PollutantsPollutants
DrugsDrugsNeurotransmittersNeurotransmitters
Chemical ThreatsChemical Threats
NH
HO
NH3+
TNT RDX
MTBE
D-lactateL-lactate
5-fluorouracil
ibuprofen
PMPA~soman
serotonin
NH3+HO
HOdopamine
N
N
NNO2
-
NO2-
NO2-
NO2-
NO2-
CH3
NO2-
O
OH
O
CH3
CH3
CH3
CH3
CH3
O
H3C
CH3
CH3
CH3
NH
NH
O
O
F
CH3
H-OOC
H3C
CH3
H
O
CH3C
O
O
H
&
[L-lactate] (µM) 0
0.5
1
40 80
Fx
Kd = 2 µM
Fx
0
0.5
1
52.5 100
Kd = 6 µM
[serotonin] (µM)
0
0.5
1
12.5 25
Kd = 2 nMxF
[TNT] (nM)
0
0.5
1
0 150 300
Fx
Kd = 4 nM
[5-fluorouracil] (nM)
Fx
0
0.5
1
50 100
Kd = 6 µM
[MTBE] (µM) 0
0.5
1
0.25 0.5
Fx
Kd = 45 nM
[PMPA] (µM)
QSAR Results for binding affinities QSAR Results for binding affinities for L-lactate & TNT Receptorsfor L-lactate & TNT Receptors
Calculated affinities from
€
log K
d
( ) = c
+ c
Δ G
elec
+ c
A + c
4
N
unsat
+ c
5
N
clash
+ c
6
s − s
0.
linear regressi oncoefficients, c…c6,obtained by a least-square s f it of t he experimenta l data; ΔGelec electrostat ic contribution;A nonpolar contact area between receptor and ligand;Nunsat number of unsatisfied hydrogen bonds i nthe ligand;Nclash number of steric clas hes between t heli gandand receptor (defi neda s contacts >5 kca/l mo );l s rati o of the volumes of the wild-type li gandto t hetarge t ligand;s0 apparen toptimum value of s for a particular li .gand
-10
-8
-6
-4
-2
0
log Kd (obs) -8 -4-6 -2
QBP
GBP
ABP
HBP
1100µM
10
101
100mM
0.1
RBP
L-lactate designs
QBP
GBP
ABP
HBP
1100µM
10
101
100mM
0.1
RBP
The use of QSARs in the predictions improves the designs: D-lactate
Construction of biological sentinels for Construction of biological sentinels for chemical threats and pollutantschemical threats and pollutants
[inducer]
exp
ress
ion modulation binary
Unicellular sentinels for chemical threats and pollutants
- + - +
Ribose
Lactate
5 Fluoro-uracil
TNT
MTBE
100 M 10 M 1 M 0.1 M 0.01 M 0.001 M
IPTG 0 M TNT
[TNT]
100 M2,4-DNT
100 M2,6-DNT
Dose Response of TNT Signaling
-1
-0.5
0
0.5
1
0 10 20 30 40 50 60
Ab
sorb
ance
210n
m
-1
-0.5
0
0.5
1
-1.5
-1
-0.5
0
0.5
1
1.5
0 10 20 30 40 50 60
Fraction #
Wt Gbp
L-Lac.G1
D-Lac.G1
KdlactateD L
none none
200µM 3µM
0.8µM 10µM
Immobilized receptors
Racemic mix
Optically pure enantiomers
0 10 20 30 40 50 60
LD
L
D
Computational design of ligand-binding sitesStrategy #2: predefined geometries
{ l, 1, 2, 1, 2, 3 }n
geometrical description of
essential features in the
complementary surface
side-chain rotamer library
+...
Site 1
Site 2
Combinatorial search
(108 sequence1012 rotamers)
Calculation #1Initial placement of PCS
on scaffold backbone
Design scaffold coordinates
Pairwise of atomic interactions
Complementarysurface
construction(1010-10200
rotamers)
Site 1
Site 2
+...
Calculation #2Complementary
surface construction(PCS + SCS)
Triose phosphate isomerase chemistry
Acknowledgements
• Mary Dwyer
• Jeff Smith
• Shahir Rizk