NMR studies on protein-nucleic acid interaction

Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations

RNA polymerase II (Pol II) forms a complex with elongation factors to proceed to the elongation stage of the transcription process. In this work, we studied the elongation factor SPT5 and explored the protein-nucleic acid interactions for the isolated systems of KOW1 and KOW4 domains of SPT5 with DNA and RNA, respectively. We performed molecular dynamics (MD) simulations using three commonly used force fields that are CHARMM c36m, AMBER ff14sb, and ff19sb. Simulations showed strong protein-nucleic acid interactions and low electrostatic binding free energies for all force fields used. RNA was found to be highly dynamic with all force fields, while DNA had relatively more stable conformations with the AMBER force fields compared to that with CHARMM. Furthermore, we performed MD simulations of the complete elongation complex using CHARMM c36m and AMBER ff19sb force fields to compare the dynamics and interactions with the isolated systems. Similarly, strong KOW1 and DNA interactions were observed in the complete elongation complex simulations and DNA was further stabilized by a network of interactions involving SPT5-KOW1, SPT4, and rpb2 of Pol II. Overall, our study showed that the differences between CHARMM and AMBER force fields strongly affect the dynamics of the nucleic acids. CHARMM provides highly flexible DNA, while AMBER largely stabilizes the DNA structure. Although the presence of the entire interaction network stabilized the DNA and decreased the differences in the results from the two force fields, the discrepancies of the force fields for smaller systems may reflect their problems in generating accurate dynamics of nucleic acids.

Expression, Purification, and Solution-State NMR Analysis of the Two Human Single-Stranded DNA-Binding Proteins hSSB1 (NABP2/OBFC2B) and hSSB2 (NAPB1/OBFC2A)

Single-stranded DNA-binding proteins (SSBs) are essential to all living organisms as protectors and guardians of the genome. Apart from the well-characterized RPA, humans have also evolved two further SSBs, termed hSSB1 and hSSB2. Over the last few years, we have used NMR spectroscopy to determine the molecular and structural details of both hSSBs and their interactions with DNA and RNA. Here we provide a detailed overview of how to express and purify recombinant versions of these important human proteins for the purpose of detailed structural analysis by high-resolution solution-state NMR.