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Most predictors (including FO, StoneHinge, and TLSMD) were able to predict the first
hinge at residues 88-89, but the second hinge was more challenging (see links from
molmovdb.org/HAG). Only TLSMD and FO1M found this hinge for the open form
(Figure 3). And only TLSMD found it for the closed form. There are two likely reasons
why the second hinge (residues 263-264) should be harder to predict. First, the motion
about that hinge involves significantly smaller displacements, and may have less to do
with intrinsic flexibility than with the influence of its large ligand, DNA. The ligand
should be particularly problematic for the closed form, co-crystallized with DNA. The
interactions between the C-terminal domain and the DNA are extensive, thus algorithms
like FO and the normal mode based predictors can be expected to do poorly since in this
implementation they do not take ligands into account.
Glutamine Binding Protein (GluBP) (open)
Morph ID: f927198-20246 PDB ID: 1GGG
HAG hinges (residues 89,90,178-182)
We will now discuss GluBP in greater detail than was given in the main text. Gram-
negative organisms have a cell envelope consisting of an outer membrane, a cell wall, a
periplasmic space, and a cytoplasmic membrane. The outer membrane acts a sieve,
limiting access of molecules to the cytoplasmic membrane. Proteins embedded in the
cytoplasmic membrane carry out functions such as lipid synthesis, protein secretion,
chemotaxis, and transport of electrons and nutrients. Nutrient transport processes can be
passive or active. In the latter case, the transport is against a concentration gradient and
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