1 | INTRODUCTION
Every two years since 1994, CASP (Critical Assessment of Structure
Prediction) has conducted a community experiment to determine the state
of the art in computing protein structure from amino acid sequence.
Participants are provided with sequence information for non-public
structures and invited to submit computed 3D structures which are then
assessed by comparison with experimental data using established metrics.
The 2020 (CASP14) experiment (1) saw the problem essentially solved for
most single protein structures (2) using a new deep learning method,
AlphaFold2 (AF2) (3). Many computed structures were competitive in
accuracy with the corresponding experimental ones. To build on these
results, the scope of CASP15 (2022) was expanded to include several new
areas where the deep learning methods hold promise for further progress
(4). One area of high significance and challenge is the modeling of
multiple conformational states of macromolecules and macromolecular
complexes. While a single conformation might be sufficient to understand
function, in other situations, the ability of macromolecules to adopt
multiple conformational states provides the basis for functional
properties.
Multiple conformations can arise in a variety of situations. One class
are those that occur under the same environmental conditions and these
fall into two main groups: ordered or intrinsically disordered proteins
/domains /regions. Disorder ensembles present unique computational
challenges and are covered by one of CASP’s sister organizations, CAID
(Critical Assessment of Intrinsic Disorder). The results of the most
recent CAID round are also reported in this CASP special issue (5).
Ordered multi-conformational structures were represented in CASP15 by
low population states of three kinases (CASP targets T1195-T1197),
investigated by NMR, and a long-lived folding intermediate of a
structured RNA molecule (target R1138).
The second and more varied class of alternative conformations are those
exerted under different conditions. Different conformational states may
be induced in the presence of different small ligands, both organic and
inorganic, or by binding to other macromolecules. Ligand binding effects
on conformation are often allosteric in that they trigger conformational
changes affecting function. For this class, CASP15 includes an ABC
transporter target with four different ligands bound, inducing three
primary conformational states (T1158 series) and an RNA target observed
in two states, one with four protein molecules bound (R1190) and the
other with six (R1189). Changes in the primary amino acid sequence, i.e.
mutations, may also induce conformational changes, and there is one such
case (T1109/10) where a single mutation induces a domain swap.
Conformation may also change depending on functional state, and targets
T1170, H1171, and H1172 are for different states of a Holliday junction
complex. Solvent changes may also induce conformational variations and
there is a pair of closely related targets (T1160/61) with conformations
observed under different crystallization conditions.
Thus, although small in number, the CASP15 ensemble targets have
provided a diverse set of multiple-conformational-state targets, and a
very interesting pilot experiment in this area.