Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
We review recent computational advances in the study of membrane proteins, focusing on those that have at least one transmembrane helix. Transmembrane protein regions are, in many respects, easier to investigate computationally than experimentally, due to the uniformity of their structure and interactions (e.g. consisting predominately of nearly parallel helices packed together) on one hand and presenting the challenges of solubility on the other. We present the progress made on identifying and classifying membrane proteins into families, predicting their structure from amino-acid sequence patterns (using many different methods), and analyzing their interactions and packing The total result of this work allows us for the first time to begin to think about the membrane protein interactome, the set of all interactions between distinct transmembrane helices in the lipid bilayer.
Lehnert
Ursula
U
Department of Molecular Blophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
Xia
Yu
Y
Royce
Thomas E
TE
Goh
Chem-Sing
CS
Liu
Yang
Y
Senes
Alessandro
A
Yu
Haiyuan
H
Zhang
Zhao Lei
ZL
Engelman
Donald M
DM
Gerstein
Mark
M
D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D023281:Genomics / Q000379:methods; D008565:Membrane Proteins / Q000032:analysis / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
D008565:Membrane Proteins