Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques.

Content Provider	Europe PMC
Author	Szpotkowski, Kamil Wójcik, Klaudia Kurzyńska-Kokorniak, Anna
Copyright Year	2023
Abstract	Protein–nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge of the biological functions and molecular mechanisms beyond the activity of the macromolecular complexes can be determined from their tertiary structures. Undoubtably, performing structural studies of protein-nucleic acid complexes is challenging, mainly because these types of complexes are often unstable. In addition, their individual components may display extremely different surface charges, causing the complexes to precipitate at higher concentrations used in many structural studies. Due to the variety of protein-nucleic acid complexes and their different biophysical properties, no simple and universal guideline exists that helps scientists chose a method to successfully determine the structure of a specific protein-nucleic acid complex. In this review, we provide a summary of the following experimental methods, which can be applied to study the structures of protein-nucleic acid complexes: X-ray and neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force microscopy (AFM), small angle scattering (SAS) methods, circular dichroism (CD) and infrared (IR) spectroscopy. Each method is discussed regarding its historical context, advancements over the past decades and recent years, and weaknesses and strengths. When a single method does not provide satisfactory data on the selected protein–nucleic acid complex, a combination of several methods should be considered as a hybrid approach; thus, specific structural problems can be solved when studying protein-nucleic acid complexes.
Journal	Computational and Structural Biotechnology Journal
Volume Number	21
PubMed Central reference number	PMC10195699
PubMed reference number	37216015
e-ISSN	20010370
DOI	10.1016/j.csbj.2023.04.028
Language	English
Publisher	Research Network of Computational and Structural Biotechnology
Publisher Date	2023-04-29
Access Restriction	Open
Rights License	This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). © 2023 The Author(s)
Subject Keyword	Nucleic acid binding proteins Protein-nucleic acid complex Nucleoproteins RNA-protein interactions DNA-protein interactions Crystallography Nuclear Magnetic Resonance (NMR) Cryogenic Electron Microscopy (cryo-EM) Atomic force microscopy (AFM) Small Angle X-ray Scattering (SAXS) Small Angle Neutron Scattering (SANS) Circular Dichroism (DC) Infrared Scpectroscopy (IR)
Content Type	Text
Resource Type	Article
Subject	Biochemistry Genetics Biophysics Biotechnology Structural Biology Computer Science Applications