Premium
Energetics and Interfacial Interactions of Spliceosomal Protein Dib1 Predicted with MD Simulations
Author(s) -
Goldstein Rachel,
Cheng Sara,
Orr Gabby,
Schreib Christian,
Cheng Kwan,
Maeder Corina
Publication year - 2019
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2019.33.1_supplement.627.2
Subject(s) - spliceosome , rna splicing , molecular dynamics , chemistry , mutant , intron , hydrogen bond , biophysics , rna , crystallography , chemical physics , biochemistry , computational chemistry , biology , molecule , gene , organic chemistry
The spliceosome is the highly dynamic macromolecular complex responsible for catalyzing the excision of introns from pre‐messenger RNA. The spliceosome consists of five small nuclear ribonucleoproteins as well as several additional proteins. As part of a complex assembly pathway, the essential protein Dib1 must leave the spliceosome. Experimental analysis has found a temperature sensitive phenotype of Dib1 (TS‐Dib1, F85A) that hinders splicing activity. This phenotype has also been hypothesized to perturb spliceosome assembly. Our current work uses atomistic molecular dynamic (MD) simulations to study the molecular interactions in the region of the spliceosome around Dib1 in order to determine what energetic and structural changes result from this point mutation. Starting with recently published cryo‐EM structures, the spliceosome was reduced to only include components in close proximity to Dib1 (either native or F85A). The reduced Dib1 structure consists of three snRNAs (U4, U5, and U6) and four proteins (Prp6, Prp8, Brr2, Prp31). Both systems, containing either native Dib1 or mutant Dib1, were simulated using atomistic MD simulations to identify energetic differences between native Dib1 and mutant TS‐Dib1. The simulation conditions mimicked the biological conditions of previous bulk splicing assays, with an aqueous solvent, 0.1 M salt, and temperature differences that have experimentally shown TS‐Dib1 inactivation. The MD simulations revealed a lower global binding energy in the TS‐Dib1 system compared to the native Dib1 system. Additionally, interfacial hydrogen bonding patterns displayed increased hydrogen bonding among Prp6, Prp8, and Dib1 in the native Dib1 system that were not present in the TS‐Dib1 system, which could contribute to the lower global binding energy. The results from the MD simulations support the experimentally observed temperature sensitivity in the TS‐Dib1 system and could help explain the role of Dib1 in spliceosome assembly. Support or Funding Information NIH R15GM120720, Robert A Welch Foundation Grant W‐1905 This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .