C
OMMUNICATION
Degenerate Interfaces in Antigen-Antibody Complexes
K.Decanniere*,T.R.Transue,A.Desmyter,D.Maes,S.Muyldermans
and L. Wyns
Vrije Universiteit Brussel
Dienst Ultrastructuur, Vlaams
Instituut voor Biotechnologie
Paardenstraat 65, B-1640
St.-Genesius Rode, Belgium
In most of the work dealing with the analysis of protein-protein inter-
faces, a single X-ray structure is available or selected, and implicitly it is
assumed that this structure corresponds to the optimal complex for this
pair of proteins. However, we have found a degenerate interface in a
high-af®nity antibody-antigen complex: the two independent complexes
of the camel variable domain antibody fragment cAb-Lys3 and its anti-
gen hen egg white lysozyme present in the asymmetric unit of our crys-
tals show a difference in relative orientation between antibody and
antigen, leading to important differences at the protein-protein interface.
A third cAb-Lys3-hen lysozyme complex in a different crystal form
adopts yet another relative orientation. Our results show that protein-
protein interface characteristics can vary signi®cantly between different
specimens of the same high-af®nity antibody-protein antigen complex.
Consideration should be given to this type of observation when trying to
establish general protein-protein interface characteristics.
# 2001 Academic Press
Keywords: immunoglobulin; heavy chain antibody; VHH; interface;
antigen binding
*Corresponding author
Interfaces
Understanding the properties of protein-protein
interaction surfaces is an important issue in protein
structure and function research. Jones & Thornton
compared the interface involved in protein-protein
interactions with other surface patches of the same
protein.
1,2
Theyshowedthattheshapeandchemi-
cal nature of protein interfaces are barely different
from other surface patches of the same protein.
Nevertheless, subtle tendencies can be observed if
the nature of the complex is taken into account,
e.g. constitutive multimeric proteins tend to be
slightly more hydrophobic at their interface. This
correlation between type of complex and interface
propertieswascon®rmedbyLoConteetal.
3
An important concept for understanding inter-
faces de®ned as early as 1945 is the requirement
forshapecomplementarity.
4
Assessmentofshape
complementarity can be conducted in various
ways. One way is the Sc parameter introduced by
Lawrence&Colman.
5
WithSc-valuesbetween0.64
and 0.68, antigen-antibody interfaces were shown
to be less complementary than other types of pro-
tein-protein complexes. This conclusion was con-
®rmed using the ``gap volume'' to measure shape
complementarity.
2
Shapecomplementaritycanalso
be assessed by calculating Voronoi volumes
around interface atoms: the volume occupied by
an atom is limited by its neighbours and can be
calculatedusingatriangulationalgorithm.
3,6,7
In
the case of perfect shape complementarity, the
volume occupied by interface atoms is as small as
the volume occupied by similar atoms situated in
the core of the protein (the atoms have a high
packing density). Using this method, differences in
shape complementarity between antibody-antigen
complexes and other types of complexes are not
apparent.
3
Besidesshapecomplementarity,speci®c
binding requires complementary patterns of sur-
facepolargroups.
8
Moreover,asubstantialfraction
of the free energy gain upon complexation comes
fromtheburialofhydrophobicresidues.
9,10
The
relative importance of these types of interactions
depends on the nature of the complex.
The biological potential of imperfect interfaces
should also be considered. The interface of a T-cell
receptor and a self peptide has been described to
E-mail address of the corresponding author:
klaas@ultr.vub.ac.be
Present address: T. R. Transue, Laboratory of
Structural Biology, MD F3-05, Niehs, NIH. PO Box
12233, Research Triangle Park, NC 27709, USA.
Abbreviations used: CDR, complementary
determining region; PDB, Protein Data Bank.
doi:10.1006/jmbi.2001.5075availableonlineathttp://www.idealibrary.comon
J. Mol. Biol. (2001) 313, 473±478
0022-2836/01/030473±6 $35.00/0 # 2001 Academic Press