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