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Structural analysis of one such antibody in complex with antigen showed that the inert CDR-H3 loop was nonetheless highly buried at the antibody antigen interface.
L36 is highly buried (ASA = 0.9%) due to its contact with L90, but it is feasible that this contact may be disrupted upon Rev-RNA binding.
The Trps in HγD-Crys are highly buried inside the hydrophobic core of the β-sheet fold.
On the other hand, residues such as ILE_H29, TYR_H53 and ASP_H99, which are already highly buried in the free form and therefore contribute less than 0.1% to the BSAFab, are still making contacts, contributing between 1.2% and 2.4% in the calculation of ICs.
Indeed, if we divide residues evenly into "hydrophobic" and "hydrophilic" classes (Kyte and Doolittle 1982), we observe that highly buried TM and EM residues with RSA ≤ 0.2 are both strongly enriched for hydrophobic residues in S. cerevisiae (76% of TM residues with RSA ≤ 0.2 are classified as hydrophobic, compared with 71% of EM residues; fig. 3 B).
Our RSA distributions calculated from structurally annotated yeast membrane proteins agree with the findings of Oberai et al., namely that TM regions tend to contain a greater proportion of "highly buried" (RSA ≤ 0.2) residues than EM regions (51% of TM residues have RSA ≤ 0.2, compared with 37% of EM residues; fig. 3 A).
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HγD-Crys has four highly conserved buried tryptophans (Trps), with two in each of the homologous β-sheet domains.
In the structure presented here, a network of five highly ordered, buried water molecules can be seen to interact with the N3 and O2 atoms in the minor groove of the DNA duplex.
The problem is that these highly successful predictions are buried in a mountain of slag.
Since his body was highly infectious, he was buried the day he died.
There are suspicions that Iraq's stockpiles of biological weapons are aboard ever-moving vans, and that its program to develop highly enriched uranium is buried deep underground.
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