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HuCal VLk 3 Problem Spots

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CDRs VL
positive Phi angles
cis/trans Pro residues
H-Bonds
V/C interf. VL
Core residues VL
Dimer interf. VL Haptens
Dimer interf. VL Oligom.
Dimer interf. VL Proteins
Antigen interf. VL Haptens
Antigen interf. VL Oligom.
Antigen interf. VL Proteins
Randomized residues VL lambda
Randomized residues VL kappa
L3: Val->Ser
exposed hydrophobic side chain, no stabilizing contacts.
L15: Pro->Leu
exposed hydrophobic side chain,
In Rei, L15 Ala->Leu was found to be strongly stabilizing(-7.0kJ/mol), L15 Ala->Pro somewhat less so (-4.5kJ/mol), therefore a stabilizing effect of Pro->Leu could be expected.
Leu->Glu was found to have a negative effect in 4/4/20
No data on how this affects FAB format
L32: Ser positive Phi angle
L33 Ser positive Phi angle
L39: Ser positive Phi angle
L67: Ala positive Phi angle
L101: Phe->xxx
4T5: Leu->Ala pos. effect on production 4D5Flu: Phe selected over ASTIV, Hag: L101 Leu->Gln strongly selected. Two different side chain conformations observed in the PDB: either pointing outwards and fully exposed (as modelled in VK3) or packing underneath Ile L147 and Val L15 (as modelled in VK1. If stability is the main problem for VK1), Phe should be retained. If the stability is good, but folding yields leave to be desired, substitution of Phe by Ala or Gln might be an option.
No data on how this affects FAB format
L103:Val->Thr
exposed hydrophobic side chain, should not affect FAB
L147: Ile->Thr
exposed hydrophobic side chain, but potentially stabilizing lateral interaction with Pro L15 and Val L101
No data on how this affects FAB format

HuCal Structure Display VLk 3

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AAAAA Homepage Zürich University Dept. of Biochemistry Plückthun Group Annemarie Honegger

Last Modified by A.Honegger Tuesday, March 25, 2008