notes 11-17-12 d 1040

2013-12-01

azim58 - notes 11-17-12 d 1040

Crystal structure of a phage library-derived single-chain Fv fragment
complexed with turkey egg-white lysozyme at 2 p 0 A resolution

notes
11-17-12

don't know what a paratope is
it's the part of the antibody that binds to the epitope

usually both light chain and heavy chain are involved in antigen binding

camelid antibodies only have heavy chain

q
The antigen-binding site of an antibody is composed
of six CDRs (L1, L2, L3, H1, H2, and H3),
that cover approximately one third of the whole
scFv sequence. The H3 segment has the greatest
variability in length, sequence, and structure.

q
four topographic
classes: concave and moderately concave
(mostly hapten binders); ridged (mostly peptide
binders); and planar (mostly protein binders).

q
anti-peptide antibodies and those that bind to
nucleotides possess a very pronounced cleft.
-I wonder ab that bind to protein have different shapes typically if they
bind to conformational epitopes or linear epitopes

q
A myc-tag for af®nity puri®-
cation was added behind the C terminus of VL.

We determined the X-ray structure of the scFv
1F9/TEL complex in order to answer the question
as to why the antigen-binding speci®city is
enhanced preferentially in TEL when the VH
domain is combined with a light chain variable
region

Kabat et al. has a certain numbering system

the linker is very flexible

q
Only ®ve CDR regions, L1,
L2, L3, H1 and H3, are involved in antigen binding.
-for this lysozyme of course

q
Data processing was done with DENZO/SCALEPACK

qModel
building was carried out with the program O

electron density maps

the high
resolution data (20.0-2.0 AÊ )

what is the unit of an angstrom again? 10^-10?

a-carbon atom tube drawing

q
representation was drawn with WebLab
ViewerPro
the representation is a stereo surface representation

q
A least-squares
superposition of three lysozyme crystal structures
in complex with their respective antibody Fv fragments
selected as examples for these three epitope
regions, together with the scFv 1F9/TEL complex
are shown in Figure 2

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