of 10
YMTHE, Volume
32
Supplemental Information
Fast, accurate ranking of engineered proteins
by target-binding propensity
using structure modeling
Xiaozhe Ding, Xinhong Chen, Erin E. Sullivan, Timothy F. Shay, and Viviana Gradinaru
1
a
Inferred LY6A
dependency
BALB/c
brain?
C57BL/6J
brain?
Modeled peptide
sequence
Ref.
Variant
name
True
*
AQTLAVPFKAQAQTG
Deverman et al.
PHP.B
True
**
DGTLAVPFKAQAQTG
Chan et al.
PHP.eB
True
*
AQSVSKPFLAQAQTG
Deverman et al.
PHP.B2
True
*
AQFTLTTPKAQAQTG
Deverman et al.
PHP.B3
True
AQTLAVPFSNPAQTG
Kumar et al.
PHP.N
True
AQTALKPFLAQAQTG
Kumar et al.
PHP.V1
True
AQTTLKPFLAQAQTG
Kumar et al.
PHP.V2
False
AQRYQGDSVAQAQTG
Kumar et al.
PHP.C1
False
AQWSTNAGYAQAQTG
Kumar et al.
PHP.C2
False
AQERVGFAQAQAQTG
Kumar et al.
PHP.C3
False
**
AQ
-------
AQAQTG
Gao et al.
AAV9
False
-
AQPHEGSSRAQAQTG
Chen et al.
MacPNS1
False
-
AQPNASVNSAQAQTG
Chen et al.
MacPNS2
False
-
AQSLDTTKGAQAQTG
Kumar et al.
NB
-
1
False
-
AQESRGLSLAQAQTG
Kumar et al.
NB
-
2
False
-
AQMIRGLDTAQAQTG
Kumar et al.
NB
-
3
False
-
AQNGDLTRSAQAQTG
Kumar et al.
NB
-
4
False
-
AQTKREIDYAQAQTG
Kumar et al.
NB
-
5
False
-
AQMHHGMEIAQAQTG
Kumar et al.
NB
-
6
False
-
AQTPRMDTFAQAQTG
Kumar et al.
NB
-
7
False
-
AQVHRDLNFAQAQTG
Kumar et al.
NB
-
8
False
-
AQTARKEEFAQAQTG
Kumar et al.
NB
-
9
* LY6A binding had been confirmed by cell binding assay
** LY6A dependency had been biochemical and genetic assays
c
b
Figure S1 Prior experimental studies revealing the receptor dependency of some brain-transducing AAV variants.
a)
AschematicshowinganAAVcapsidbindingtoablood-brainbarrier(BBB)receptorthatisonlyexpressedatahighlevel
on the endothelial cells of certain mouse strains
37
39
.
b)
AschematicshowinghowwecaninferwhetheranAAVcapsidcanuse
LY6A, a mouse BBB receptor, by characterizing its brain transduction across di
erent strains. A capsid with strain-restricted brain
transduction in C57BL/6J mice is likely LY6A-dependent, while a capsid with cross-strain brain transduction or which does not
transduce the brain is not LY6A-dependent.
c)
Atablesummarizingall22capsidsusedinFigure
2
with their source literature,
sequence, brain transduction profile, and inferred LY6A dependency.
2
a
b
c
d
Figure S2 Distributions of interface energy scores in example proteins of interest.
Histograms showing distributions
of
a, b)
B
POI
0
and
c, d)
B
POI
0
averaged across replicates for a LY6A binder, PHP.eB, and a non-binder, AAV9, from the AAV
dataset.
a
b
Figure S3 Heatmaps representing score matrices of AF-Multimer-APPRAISE 1.1 and ESMFold-APPRAISE 1.2.