title: Recognition of the spliceosomal branch site RNA helix on the basis of surface and electrostatic features.
abstract: We have investigated electrostatic and surface features of an essential region of the catalytic core of the spliceosome, the eukaryotic precursor messenger (pre-m)RNA splicing apparatus. The nucleophile for the first of two splicing reactions is the 2'-hydroxyl (OH) of the ribose of a specific adenosine within the intron. During assembly of the spliceosome's catalytic core, this adenosine is positioned by pairing with a short region of the U2 small nuclear (sn)RNA to form the pre-mRNA branch site helix. The solution structure of the spliceosomal pre-mRNA branch site [Newby,M.I. and Greenbaum,N.L. (2002) Nature Struct. Biol., 9, 958-965] showed that a phylogenetically conserved pseudouridine (psi) residue in the segment of U2 snRNA that pairs with the intron induces a markedly different structure compared with that of its unmodified counterpart. In order to achieve a more detailed understanding of the factors that contribute to recognition of the spliceosome's branch site helix and activation of the nucleophile for the first step of pre-mRNA splicing, we have calculated surface areas and electrostatic potentials of psi-modified and unmodified branch site duplexes. There was no significant difference between the total accessible area or ratio of total polar:nonpolar groups between modified and unmodified duplexes. However, there was substantially greater exposure of nonpolar area of the adenine base, and less exposure of the 2'-OH, in the psi-modified structure. Electrostatic potentials computed using a hybrid boundary element and finite difference nonlinear Poisson-Boltzmann approach [Boschitsch, A.H. and Fenley, M.O. (2004) J. Comput. Chem., 25, 935-955] revealed a region of exceptionally negative potential in the major groove surrounding the 2'-OH of the branch site adenosine. These surface and electrostatic features may contribute to the overall recognition of the pre-mRNA branch site region by other components of the splicing reaction.
authors.affiliation: Department of Chemistry and Biochemistry, Florida State University Tallahassee FL 32306-4390, USA.
authors.forename: Darui
authors.initials: D
authors.lastname: Xu
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Greenbaum
authors.forename: Marcia O
authors.initials: MO
authors.lastname: Fenley
mesh_terms: D000241:Adenosine / Q000737:chemistry; D020029:Base Pairing; D007438:Introns; D008958:Models, Molecular; D011560:Pseudouridine / Q000737:chemistry; D012322:RNA Precursors / Q000737:chemistry*; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry*; D012342:RNA, Small Nuclear / Q000737:chemistry*; D017381:Spliceosomes / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; C405484:U2 small nuclear RNA; D011560:Pseudouridine; D000241:Adenosine
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