EPR assessment of protein sites for incorporation of Gd(III) MRI contrast labels

Impact of Cellular Crowding on Protein Structural Dynamics Investigated by EPR Spectroscopy

The study of how the intracellular medium influences protein structural dynamics and protein-protein interactions is a captivating area of research for scientists aiming to comprehend biomolecules in their native environment. As the cellular environment can hardly be reproduced in vitro, direct investigation of biomolecules within cells has attracted growing interest in the past two decades. Among magnetic resonances, site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy (SDSL-EPR) has emerged as a powerful tool for studying the structural properties of biomolecules directly in cells. Since the first in-cell EPR experiment was reported in 2010, substantial progress has been made, and this Review provides a detailed overview of the developments and applications of this spectroscopic technique. The strategies available for preparing a cellular sample and the EPR methods that can be applied to cells will be discussed. The array of spin labels available, along with their strengths and weaknesses in cellular contexts, will also be described. Several examples will illustrate how in-cell EPR can be applied to different biological systems and how the cellular environment affects the structural and dynamic properties of different proteins. Lastly, the Review will focus on the future developments expected to expand the capabilities of this promising technique.

A water-soluble luminescent tris(2,4,6-trichlorophenyl)methyl radical-carbazole dyad

Organic luminescent radicals are a new class of materials with potential applications not only in light-emitting devices but also in the biochemistry field. New tris(2,4,6-trichlorophenyl)methyl (TTM) radicals with alkoxy-substituted carbazole donors were synthesized and characterized. PEG-substituted carbazole-TTM was found to be water-soluble. The water-soluble TTM radical aqueous solution showed fluorescence at 777 nm and the ability to shorten the longitudinal relaxation time (T1) of water. The concept of water-soluble luminescent radicals is expected to be used to develop a potential fluorescence and MR dual-use imaging moiety.

Spectroscopically Orthogonal Spin Labels in Structural Biology at Physiological Temperatures

Electron paramagnetic resonance spectroscopy (EPR) is mostly used in structural biology in conjunction with pulsed dipolar spectroscopy (PDS) methods to monitor interspin distances in biomacromolecules at cryogenic temperatures both in vitro and in cells. In this context, spectroscopically orthogonal spin labels were shown to increase the information content that can be gained per sample. Here, we exploit the characteristic properties of gadolinium and nitroxide spin labels at physiological temperatures to study side chain dynamics via continuous wave (cw) EPR at X band, surface water dynamics via Overhauser dynamic nuclear polarization at X band and short-range distances via cw EPR at high fields. The presented approaches further increase the accessible information content on biomolecules tagged with orthogonal labels providing insights into molecular interactions and dynamic equilibria that are only revealed under physiological conditions.

Understanding the Exchange of Systemic HDL Particles Into the Brain and Vascular Cells Has Diagnostic and Therapeutic Implications for Neurodegenerative Diseases

High-density lipoproteins (HDLs) are complex, heterogenous lipoprotein particles, consisting of a large family of apolipoproteins, formed in subspecies of distinct shapes, sizes, and functions and are synthesized in both the brain and the periphery. HDL apolipoproteins are important determinants of Alzheimer’s disease (AD) pathology and vascular dementia, having both central and peripheral effects on brain amyloid-beta (Aβ) accumulation and vascular functions, however, the extent to which HDL particles (HLD-P) can exchange their protein and lipid components between the central nervous system (CNS) and the systemic circulation remains unclear. In this review, we delineate how HDL’s structure and composition enable exchange between the brain, cerebrospinal fluid (CSF) compartment, and vascular cells that ultimately affect brain amyloid metabolism and atherosclerosis. Accordingly, we then elucidate how modifications of HDL-P have diagnostic and therapeutic potential for brain vascular and neurodegenerative diseases.

A systematic review of the biodistribution of biomimetic high-density lipoproteins in mice

For the past two decades, biomimetic high-density lipoproteins (b-HDL) have been used for various drug delivery applications. The b-HDL mimic the endogenous HDL, and therefore possess many attractive features for drug delivery, including high biocompatibility, biodegradability, and ability to transport and deliver their cargo (e.g. drugs and/or imaging agents) to specific cells and tissues that are recognized by HDL. The b-HDL designs reported in the literature often differ in size, shape, composition, and type of incorporated cargo. However, there exists only limited insight into how the b-HDL design dictates their biodistribution. To fill this gap, we conducted a comprehensive systematic literature search of biodistribution studies using various designs of apolipoprotein A-I (apoA-I)-based b-HDL (i.e. b-HDL with apoA-I, apoA-I mutants, or apoA-I mimicking peptides). We carefully screened 679 papers (search hits) for b-HDL biodistribution studies in mice, and ended up with 24 relevant biodistribution profiles that we compared according to b-HDL design. We show similarities between b-HDL biodistribution studies irrespectively of the b-HDL design, whereas the biodistribution of the b-HDL components (lipids and scaffold) differ significantly. The b-HDL lipids primarily accumulate in liver, while the b-HDL scaffold primarily accumulates in the kidney. Furthermore, both b-HDL lipids and scaffold accumulate well in the tumor tissue in tumor-bearing mice. Finally, we present essential considerations and strategies for b-HDL labeling, and discuss how the b-HDL biodistribution can be tuned through particle design and administration route. Our meta-analysis and discussions provide a detailed overview of the fate of b-HDL in mice that is highly relevant when applying b-HDL for drug delivery or in vivo imaging applications.

In cell Gd3+-based site-directed spin labeling and EPR spectroscopy of eGFP

A newly synthesized Gd³⁺ chelate complex allows in cell spin labeling and detection of eGFP by EPR spectroscopy.

Lipoproteins and lipoprotein mimetics for imaging and drug delivery

Lipoproteins are a set of natural nanoparticles whose main role is the transport of fats within the body. While much work has been done to develop synthetic nanocarriers to deliver drugs or contrast media, natural nanoparticles such as lipoproteins represent appealing alternatives. Lipoproteins are biocompatible, biodegradable, non-immunogenic and are naturally targeted to some disease sites. Lipoproteins can be modified to act as contrast agents in many ways, such as by insertion of gold cores to provide contrast for computed tomography. They can be loaded with drugs, nucleic acids, photosensitizers or boron to act as therapeutics. Attachment of ligands can re-route lipoproteins to new targets. These attributes render lipoproteins attractive and versatile delivery vehicles. In this review we will provide background on lipoproteins, then survey their roles as contrast agents, in drug and nucleic acid delivery, as well as in photodynamic therapy and boron neutron capture therapy.

A simple approach to a new T8-POSS based MRI contrast agent

A simple synthesis of a new nanoglobular T₈-silsesquioxane based contrast agent for the application in MRI is reported.

X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

INTRODUCTION

Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology.

AREAS COVERED

This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions.

EXPERT OPINION

X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.

Electron paramagnetic resonance: a powerful tool to support magnetic resonance imaging research

The purpose of this paper is to describe some of the areas where electron paramagnetic resonance (EPR) has provided unique information to MRI developments. The field of application mainly encompasses the EPR characterization of MRI paramagnetic contrast agents (gadolinium and manganese chelates, nitroxides) and superparamagnetic agents (iron oxide particles). The combined use of MRI and EPR has also been used to qualify or disqualify sources of contrast in MRI. Illustrative examples are presented with attempts to qualify oxygen sensitive contrast (i.e. T1 - and T2 *-based methods), redox status or melanin content in tissues. Other areas are likely to benefit from the combined EPR/MRI approach, namely cell tracking studies. Finally, the combination of EPR and MRI studies on the same models provides invaluable data regarding tissue oxygenation, hemodynamics and energetics. Our description will be illustrative rather than exhaustive to give to the readers a flavour of 'what EPR can do for MRI'.