Jd. Olsen et Cn. Hunter, PROTEIN-STRUCTURE MODELING OF THE BACTERIAL LIGHT-HARVESTING COMPLEX, Photochemistry and photobiology, 60(6), 1994, pp. 521-535
Protein structure modelling offers a method of obtaining 3-dimensional
information that can be tested and used to plan mutagenesis experimen
ts when a crystallographically determined structure is not available.
At its simplest a model may consist of little more than a secondary st
ructure prediction coupled with a determination of the likely regions
of transmembrane/membrane surface/globular configuration. These method
s can yield an interesting topology map of the protein, which places t
he residues in their likely positions with respect to, for example, th
e membrane interface. If it is a member of a large family of related p
roteins then aligned protein sequences can be used to predict the resi
dues that have an important function as these will be largely conserve
d in the alignments. Using all these methods a model can be constructe
d (using for example, the Nicholson Molecular Modelling Kit) to visual
ize the proposed structure in three dimensions following the premise o
f good design, that is, avoiding obvious steric clashes, packing of he
lices in a realistic manner, observing the correct II-bond lengths, et
c. In this latter exercise the review of Chothia (Annu. Rev. Biochem.
53, 537-572, 1984) of the principles of protein structure is particula
rly helpful as it clearly sets out how proteins pack and their preferr
ed configuration. There is a wealth of information about individual am
ino acid conformational preferences and observed frequencies of occurr
ence in known protein structures, which can help decide how the residu
es in the model can be oriented. In this article we have collated the
various protein models of the bacterial light-harvesting complexes and
present our own model, which is a synthesis of the available biophysi
cal data and theoretical predictions, and show its performance in expl
aining recent results of site-directed mutants of the LH1 and LH2 ligh
t-harvesting complexes of Rhodobacter sphaeroides.