Publication Date

Spring 2026

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Chemistry

Advisor

Brooke Lustig; Emma Carroll; Ningkun Wang

Abstract

Here we explore the role of bridging waters and ions in protein-RNA complexes. From an initial set of 33 high-resolution X-ray crystal structures, 17 were identified such that protein-RNA complex and component protein and RNA chains were found within 1 pH unit as indicated by crystallization conditions and their diffraction temperatures meeting one of two ranges: above or below freezing. To define an even more realistic set, 12 unbound-unbound and unbound-pseudo-unbound complexes from the 17-set were studied, showing the large fraction of complexes indicating more protein and RNA water hydrogen bonding in their actual interfacial regions as opposed to those corresponding individually to their unbound components. For the original 33-set, interfacial and bridging water hydrogen bonds (H-bonds) show correlation with buried surface area (BSA) under low ion conditions, whereas correlations are for the 33-set as well as the other two filtered subsets, weak or absent under high ion conditions. This suggests the binding of certain complexes is influenced by ion environments. Most of these complexes contain significant interfacial water hydrogen bonding and include waters that bridge amino acids and ribonucleotides. Future studies will extend these analyses using machine learning approaches applied to a larger and more diverse set of protein-RNA complexes and their respective unbound protein and RNA chains.

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