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Figure 2.
Fig. 2. tereorepresentationof theALCAMDl A ALCAMDl monomer,backboneshown as a solid ribbon. The
termini (N, C),the faces A'GFCC'C, green; BED, blue), andthe CDR-analogous loops (1-4, yellow) are labeled.
Positionsofpotential N-linked glycosylation sites are colored in magenta. B Possible Fv-like homodier monomers col-
ored in ray and pink, ALCAMDlatthetopand thegraymonoer at thebottom have thesameorientation.
The spatialarrangementofcomplementary negatively charged (red), positively charged (blue), and hydrophobic (gold) resi-
duesthought tobe consistent with Fv-like dimerization (as discussed in he text) can be seen. Modeling methods: For computer
graphics, model building, and energy minimizations, the InsightWDiscover package (version 2.3.0.; Biosym Technologies,
San was used. Loop conformations were modeled by conformational search using COGEN (version ) (Bruccoleri &
Novotny, 1992). For each loop,theconformation minimum solvent-accessible surface within 3 kcal/mol of the energy min-
imum conformation was selected. Side-chain conformations of surface residues were modeled using low-energy side-chain rota-
mers (Ponder & Richards, 1987). Conservative side-chain replacements in core regions were modeled in conformations as similar
as possible tothe originl residue. The initially assembled model was subjected to someminor minimization (until the
RMS ofthe energy function was - 1.5 kcal/mol/A) to relieve stereochemical constraints.This resulted in a cumula-
tive proteinbackbone RMS deviation (of th &strands to thestructuraltemplate)of less than .5 A.
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