Exploring hydrophobic sites in proteins with xenon or krypton

Abstract

X-ray diffraction is used to study the binding of xenon and krypton to a variety of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from Bacillus licheniformis; cutinase from Fusarium solani; collagenase from Hypoderma lineatum; hen egg lysozyme, the lipoamide dehydrogenase domain from the outer membrane protein P64k from Neisseria meningitidis; urate-oxidase from Aspergillus flavus, mosquitocidal delta-endotoxin CytB from Bacillus thuringiensis and the ligand-binding domain of the human nuclear retinoid-X receptor RXR-alpha. Under gas pressures ranging from 8 to 20 bar, xenon is able to bind to discrete sites in hydrophobic cavities, ligand and substrate binding pockets, and into the pore of channel-like structures. These xenon complexes can be used to map hydrophobic sites in proteins, or as heavy-atom derivatives in the isomorphous replacement method of structure determination.

Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography

“…The use of noble gas pressurized crystallography is a way to characterize hydrophobic cavities 54 and in recent structures of Ngb under pressurized xenon 43, 44 , it was shown that the xenon atom in site II is lined by the five hydrophobic residues precisely forming the Ngb mechanical nucleus. Moreover, Xe still binds in this site when CO is bound and the heme has slid 43 .…”

A Genetically Encoded β‐Lactamase Reporter for Ultrasensitive 129Xe NMR in Mammalian Cells

“…[10] The promiscuous interactions of xenon with many proteins have also been investigated by the X-ray diffraction of protein crystals under high Xe pressure, where xenon can occupy hydrophobic cavities, substrate-binding sites, and also channel pores. [11] Notably, these are weak interactions, with hemoglobin and myoglobin exhibiting the highest reported xenon association constants of around 200 M −1 at rt. [12] In our search for a versatile genetically encoded reporter for Hyper-CEST NMR, we targeted a candidate protein TEM-1 β-lactamase (bla) based on its well-established allosteric site whose size and hydrophobicity suggest it to be a good target for Xe exchange.…”

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

“…Variations of this approach involve, for example, the use of the heavy-metal clusters4, especially suitable for structures of very large macromolecular complexes, the gaseous xenon or krypton pressurized into native crystals5, or the short soaking in salts of halides6 (Br or I). It is also possible to obtain useful anomalous phasing signal from sulfur of Cys and Met naturally occurring in proteins789 or from phosphorus in nucleic acids10.…”