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.