Table 1 Rationale for CDR design

CDR1

 26

Gly

–

Gly

Conserved (our own analysis). An outlier in the Ramachandran plot. Keep fixed

 27

Gly

DMY

Ala:2 Asn:2 Asp:2

Ser:2 Thr:2 Tyr:2

An outlier in the Ramachandran plot. Randomize, but keep it small. The degenerate codon includes also Tyr

 28

Ser

VRN

Arg:6 Asn:2 Asp:2

Gln:2 Glu:2 Gly:4

His:2 Lys:2 Ser:2

Surface-exposed side chain. Set it variable, but polar

 29

Glu

 30

Tyr

HWY

Asn:2 His:2 Ile:2

Leu:2 Phe:2 Tyr:2

It is packed against the extremes of CDR1. Keep it mostly big and hydrophobic/aromatic

 31

Ser

VRN

see above

Surface-exposed side chain. Set it variable, but polar

 32

Tyr

–

Tyr

Buried aa playing an important packing role. Keep fixed

 33

Ser

DMY

see above

It’s placed on an alpha turn, outside the binding site. Keep it mostly small, as the original aa

 34

Thr

VNN

Ala:4 Arg:6 Asn:2 Asp:2 Gln:2 Glu:2 Gly:4 His:2 Ile:3 Leu:4 Lys:2 Met:1 Pro:4 Ser:2 Thr:4 Val:4

Points “upwards” at the base of CDR1. Set it very variable

 35

Phe

–

Phe

Buried aa playing an important packing role. Keep fixed

 36

Ser

KMY

Ala:2 Asp:2 Ser:2 Tyr:2

Support for CDR H3 (found also making a Cys bridge with CDR H3). Becomes buried by long CDRs 3. Small aa are commonly found, as well as Tyr

CDR2

 53

Ala

–

Ala

Within a β-sheet. Packed with the long CDR3. Keep fixed

 54

Ile

–

Ile

Very conserved, buried aa playing an important packing role. Keep fixed

 55

Ala

KMY

see above

Interacting with the bent CDR3 in the original Nb. Ser and Tyr are commonly found, as well as small aa

 56

Ser

WBG

Arg:1 Leu:1 Met:1

Ser:1 Thr:1 Trp:1

Small aa side chains, like Ser and Thr, remain partially buried. The larger amino acids in the set would pack against CDR1 and the N-ter of CDR3

 57

Met

VRN

see above

Surface-exposed side chain. Set it variable, but polar

 58, 59

Gly

–

Gly

Conserved pair of residues, outliers in the Ramachandran plot. Keep fixed

 60

Leu

ADM

Arg:1 Asn:1 Ile:2

Lys:1 Ser:1

Combines long charged aa. that can protrude upwards with small polar aa. Arg, Asn Ile and Ser are among the most frequently found aa at this position

CDR3

 VNN VRN WMY VRN WMY VNN WMY VRN WMY VNN WMY TWY VRN TMY

WMY: Asn:2 Ser:2 Thr:2 Tyr:2

TWY: Phe:2 Tyr:2

TMY: Ser:2 Tyr:2

B = C, G, T

H = A, C, T

M = A, C

R = A, G

V = A, C, G

Y = C, T

D = A, G, T

K = G, T

N = A, C, G, T

S = C, G

W = A, T