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Ser and Thr Residues Modulate the Conformation of Pro-Kinked Transmembrane -Helices

Xavier Deupi ^*, Mireia Olivella ^*, Cedric Govaerts , Juan Antonio Ballesteros , Mercedes Campillo ^* and Leonardo Pardo ^*

^* Laboratori de Medicina Computacional, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Recherche Interdisciplinaire en Biologie Humaine et Nucléaire, Université Libre de Bruxelles, Campus Erasme, B-1070 Bruxelles, Belgium; and Novasite Pharmaceuticals, San Diego, California

Correspondence: Address reprint requests to Dr. Leonardo Pardo, Unitat de Bioestadística, Edifici M, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain. Tel.: 3493-581-2797; E-mail: Leonardo.Pardo{at}uab.es.

Functionally required conformational plasticity of transmembrane proteins implies that specific structural motifs have been integrated in transmembrane helices. Surveying a database of transmembrane helices and the large family of G-protein coupled receptors we identified a series of overrepresented motifs associating Pro with either Ser or Thr. Thus, we have studied the conformation of Pro-kinked transmembrane helices containing Ser or Thr residues, in both g+ and g- rotamers, by molecular dynamics simulations in a hydrophobic environment. Analysis of the simulations shows that Ser or Thr can significantly modulate the deformation of the Pro. A series of motifs, such as (S/T)P and (S/T)AP in the g+ rotamer and the TAP and PAA(S/T) motifs in the g- rotamer, induce an increase in bending angle of the helix compared to a standard Pro-kink, apparently due to the additional hydrogen bond formed between the side chain of Ser/Thr and the backbone carbonyl oxygen. In contrast, (S/T)AAP and PA(S/T) motifs, in both g+ and g-, and PAA(S/T) in g+ rotamers decrease the bending angle of the helix by either reducing the steric clash between the pyrrolidine ring of Pro and the helical backbone, or by adding a constrain in the form of a hydrogen bond in the curved-in face of the helix. Together with a number of available experimental data, our results strongly suggest that association of Ser and Thr with Pro is commonly used in transmembrane helices to accommodate the structural needs of specific functions.

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