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Abstract: Here we report a successful use of a recently developed isoprenoid-chained lipid family for in meso crystallization of membrane proteins. The isoprenoid-chained lipid 1-O-(3,7,11,15-tetramethylhexadecyl)-β–d-xyloside (β-XylOC16+4) used as a host lipid for in meso crystallization provided high quality bacteriorhodopsin (bR) crystals (P63 space group) diffracting to high resolution and characterized by low twinning ratio. β-XylOC16+4 has an isoprenoid chain with methyl branches at each 4th position and a xylose group in the water-soluble part. These peculiarities make the lipid clearly distinguishable in the bR crystalline lattice and provides a unique opportunity to study the role of the host lipid in the in meso crystallization. We conclude that β-XylOC16+4 may have a general application for in meso crystallization for a wide range of membrane proteins. The cubic phase of β-XylOC16+4 is present over a wide range of temperatures and is stable at low temperature (down to about 8°C). This opens up the possibility of using temperature as a tool for the optimization of in meso crystallization with additional advantages for the crystallization of membrane proteins at lower temperatures where the proteins of interest may be more stable. [ABSTRACT FROM AUTHOR]

Dihydroxy acid leukotriene (LTB4) and cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are inflammatory mediators derived from arachidonic acid via the 5-lipoxygenase pathway. While structurally similar, these two types of leukotrienes (LTs) exert their functions through interactions with two distinct G protein-coupled receptor (GPCR) families, BLT and CysLT receptors, which share low sequence similarity and belong to phylogenetically divergent GPCR groups. Selective antagonism of LT receptors has been proposed as a promising strategy for the treatment of many inflammation-related diseases including asthma and chronic obstructive pulmonary disease, rheumatoid arthritis, cystic fibrosis, diabetes, and several types of cancer. Selective CysLT1R antagonists are currently used as antiasthmatic drugs, however, there are no approved drugs targeting CysLT2 and BLT receptors. In this review, we highlight recently published structures of BLT1R and CysLTRs revealing unique structural features of the two receptor families. X-ray and cryo-EM data shed light on their overall conformations, differences in functional motifs involved in receptor activation, and details of the ligand-binding pockets. An unexpected binding mode of the selective antagonist BIIL260 in the BLT1R structure makes it the first example of a compound targeting the sodium-binding site of GPCRs and suggests a novel strategy for the receptor activity modulation. Taken together, these recent structural data reveal dramatic differences in the molecular architecture of the two LT receptor families and pave the way to new therapeutic strategies of selective targeting individual receptors with novel tool compounds obtained by the structure-based drug design approach. [ABSTRACT FROM AUTHOR]

Flavin-binding fluorescent proteins are promising genetically encoded tags for microscopy. However, spectral properties of their chromophores (riboflavin, flavin mononucleotide, and flavin adenine dinucleotide) are notoriously similar even between different protein families, which limits applications of flavoproteins in multicolor imaging. Here, we present a palette of 22 finely tuned fluorescent tags based on the thermostable LOV domain from Chloroflexus aggregans. We performed site saturation mutagenesis of three amino acid positions in the flavin-binding pocket, including the photoactive cysteine, to obtain variants with fluorescence emission maxima uniformly covering the wavelength range from 486 to 512 nm. We demonstrate three-color imaging based on spectral separation and two-color fluorescence lifetime imaging of bacteria, as well as two-color imaging of mammalian cells (HEK293T), using the proteins from the palette. These results highlight the possibility of fine spectral tuning of flavoproteins and pave the way for further applications of flavin-binding fluorescent proteins in fluorescence microscopy. [ABSTRACT FROM AUTHOR]

Cytochromes P450 (CYP) are a family of membrane proteins involved in the production of endogenous molecules and the metabolism of xenobiotics. It is well-known that the composition of the membrane can influence the activity and orientation of CYP proteins. However, little is known about how membrane composition affects the ligand binding properties of CYP. In this study, we utilized surface plasmon resonance and fluorescence lifetime analysis to examine the impact of membrane micro-environment composition on the interaction between human microsomal CYP51 (CYP51A1) and its inhibitor, luteolin 7,3′-disulphate (LDS). We observed that membranes containing cholesterol or sphingomyelin exhibited the lowest apparent equilibrium dissociation constant for the CYP51A1-LDS complex. Additionally, the tendency for relation between kinetic parameters of the CYP51A1-LDS complex and membrane viscosity and overall charge was observed. These findings suggest that the specific composition of the membrane, particularly the presence of cholesterol and sphingomyelin, plays a vital role in regulating the interaction between CYP enzymes and their ligands. [Display omitted] • fatty acid chain length is important for CYP-ligand interactions; • the presence of cholesterol and sphingomyelin in the membrane affect the CYP-ligand interactions; • both ligand and membrane overall charges are important for the CYP-ligand interaction; • there is an anticorrelation between the viscosity of the model membrane and the koff of the CYP51A1-LDS complex. [ABSTRACT FROM AUTHOR]

In our pursuit of developing novel analogs of anthracyclines with enhanced antitumor efficacy and safety, we have designed a synthesis scheme for 4,11-dihydroxy-5,10-dioxocyclopenta[ b ]anthracene-2-carboxamides. These newly synthesized compounds exhibit remarkable antiproliferative potency against various mammalian tumor cell lines, including those expressing activated mechanisms of multidrug resistance. The structure of the diamine moiety in the carboxamide side chain emerges as a critical determinant for anticancer activity and interaction with key targets such as DNA, topoisomerase 1, and ROS induction. Notably, the introduced modification to the doxorubicin structure results in significantly increased lipophilicity, cellular uptake, and preferential distribution in lysosomes. Consequently, while maintaining an impact on anthracyclines targets, these novel derivatives also demonstrate the potential to induce cytotoxicity through pathways associated with lysosomes. In summary, derivatives of cyclic diamines, particularly 3-aminopyrrolidine, can be considered a superior choice compared to aminosugars for incorporation into natural and semi-synthetic anthracyclines or new anthraquinone derivatives, aiming to circumvent efflux-mediated drug resistance. [Display omitted] • • New cyclopentane-fused anthraquinone derivatives have been designed and synthesized. • • Selected compounds have strong antiproliferative potency and circumvent Pgp-mediated efflux. • • Derivative 9 has increased lipophilicity and faster cellular uptake than doxorubicin. • • Terminal amino group in the side chain is crucial for DNA binding and Top1 inhibition. [ABSTRACT FROM AUTHOR]

Photoactive biological systems modify the optical properties of their chromophores, known as spectral tuning. Determining the molecular origin of spectral tuning is instrumental for understanding the function and developing applications of these biomolecules. Spectral tuning in flavin-binding fluorescent proteins (FbFPs), an emerging class of fluorescent reporters, is limited by their dependency on protein-bound flavins, whose structure and hence electronic properties cannot be altered by mutation. A blue-shifted variant of the plantderived improved light, oxygen, voltage FbFP has been created by introducing a lysine within the flavin-binding pocket, but the molecular basis of this shift remains unconfirmed. We here structurally characterize the blue-shifted improved light, oxygen, voltage variant and construct a new blue-shifted CagFbFP protein by introducing an analogous mutation. X-ray structures of both proteins reveal displacement of the lysine away from the chromophore and opening up of the structure as instrumental for the blue shift. Site saturation mutagenesis and high-throughput screening yielded a redshifted variant, and structural analysis revealed that the lysine side chain of the blue-shifted variant is stabilized close to the flavin by a secondary mutation, accounting for the red shift. Thus, a single additional mutation in a blue-shifted variant is sufficient to generate a red-shifted FbFP. Using spectroscopy, X-ray crystallography, and quantum mechanics molecular mechanics calculations, we provide a firm structural and functional understanding of spectral tuning in FbFPs. We also show that the identified blue- and red-shifted variants allow for two-color microscopy based on spectral separation. In summary, the generated blue- and red-shifted variants represent promising new tools for application in life sciences. [ABSTRACT FROM AUTHOR]

• GPCRs are highly dynamic proteins that sample multiple conformational states. • Dynamic behavior of GPCRs can be described using the concept of energy landscapes. • Understanding signaling mechanisms requires both structure and dynamics. • New approaches uncover GPCR dynamics in population and at a single molecule level. G protein-coupled receptors (GPCRs) constitute the largest superfamily of membrane proteins that are involved in regulation of sensory and physiological processes and implicated in many diseases. The last decade revolutionized the GPCR field by unraveling multiple high-resolution structures of many different receptors in complexes with various ligands and signaling partners. A complete understanding of the complex nature of GPCR function is, however, impossible to attain without combining static structural snapshots with information about GPCR dynamics obtained by complementary spectroscopic techniques. As illustrated in this review, structure and dynamics studies are now paving the way for understanding important questions of GPCR biology such as partial and biased agonism, allostery, oligomerization, and other fundamental aspects of GPCR signaling. [ABSTRACT FROM AUTHOR]