Elucidation of the disulfide folding pathway of hirudin by a topology-based approach

A theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favour the progressive establishment of native interactions. At variance with traditional approaches based on native topology, not all native bonds are treated in the same way; in particular, a suitable energy term is introduced to account for the special strength of disulfide bonds (irrespective of whether they are native or not) as well as their ability to undergo intra-molecular reshuffling. The model thus possesses the minimal ingredients necessary to investigated the much debated issue of whether the re-folding process occurs through partially structured intermediates with native or non-native disulfide bonds. This strategy is applied to a context of particular interest, the re-folding process of Hirudin, a thrombin-specific protease inhibitor, for which conflicting folding pathways have been proposed. We show that the only two parameters in the model (temperature and disulfide strength) can be tuned to reproduce well a set of experimental transitions between species with different number of formed disulfide. This model is then used to provide a characterisation of the folding process and a detailed description of the species involved in the rate-limiting step of Hirudin refolding.Comment: 14 pages, 9 figure

Crystal field, ligand field, and interorbital effects in two-dimensional transition metal dichalcogenides across the periodic table

Two-dimensional transition metal dichalcogenides (TMDs) exist in two polymorphs, referred to as $1T$ and $1H$, depending on the coordination sphere of the transition metal atom. The broken octahedral and trigonal prismatic symmetries lead to different crystal and ligand field splittings of the $d$ electron states, resulting in distinct electronic properties. In this work, we quantify the crystal and ligand field parameters of two-dimensional TMDs using a Wannier-function approach. We adopt the methodology proposed by Scaramucci et al. [A. Scaramucci et al., J. Phys.: Condens. Matter 27, 175503 (2015)]. that allows to separate various contributions to the ligand field by choosing different manifolds in the construction of the Wannier functions. We discuss the relevance of the crystal and ligand fields in determining the relative stability of the two polymorphs as a function of the filling of the $d$-shell. Based on the calculated parameters, we conclude that the ligand field, while leading to a small stabilizing factor for the $1H$ polymorph in the $d^1$ and $d^2$ TMDs, plays mostly an indirect role and that hybridization between different $d$ orbitals is the dominant feature. We investigate trends across the periodic table and interpret the variations of the calculated crystal and ligand fields in terms of the change of charge-transfer energy, which allows developing simple chemical intuition.Comment: 16 pages, 14 figure

Lattice Imaging of Self-Assembled Monolayers of Partially Fluorinated Disulfides and Thiols on Sputtered Gold by Atomic Force Microscopy

The structure of self-assembled monolayers (SAMs) of various fluorinated disulfides, perfluoroalkylamide thiols, and a mixed alkyl perfluoroalkylamide disulfide on sputtered gold was studied by atomic force microscopy (AFM). AFM, performed both in air and in ethanol, revealed the monolayer structure with molecular resolution on the polycrystalline gold substrates. For all partially fluorinated disulfides containing ester groups, a hexagonal lattice with a lattice constant of 5.8-5.9 Å was found. A mixed alkyl perfluoroalkylamide disulfide formed a hexagonal lattice of a slightly larger lattice constant (6.1 Å), whereas the lattice observed for fluorinated thiols containing an amide group was either hexagonal (5.7-5.8 Å) or distorted hexatic (5.6, 6.2, 5.6 Å), depending on the length of the perfluoroalkane segment and the imaging force. The observed deviation from hexagonal symmetry is attributed to the distorting effect of hydrogen bonding between neighboring amide groups within the monolayer. For short perfluoroalkane segments the distortion is observed at low imaging forces, whereas for long perfluoroalkane segments significantly higher imaging forces are necessary in order to observe the distortion. The force dependence of the measured lattice symmetries for different chain lengths suggests that the AFM tip penetrates into the SAM and probes at least partially the interior of the SAM

Review

The chalcogen elements oxygen, sulfur, and selenium are essential constituents of side chain functions of natural amino acids. Conversely, no structural and biological function has been discovered so far for the heavier and more metallic tellurium element. In the methionine series, only the sulfur-containing methionine is a proteinogenic amino acid, while selenomethionine and telluromethionine are natural amino acids that are incorporated into proteins most probably because of the tolerance of the methionyl-tRNA synthetase; so far, methoxinine the oxygen analogue has not been discovered in natural compounds. Similarly, the chalcogen analogues of tryptophan and phenylalanine in which the benzene ring has been replaced by the largely isosteric thiophene, selenophene, and more recently, even tellurophene are fully synthetic mimics that are incorporated with more or less efficiency into proteins via the related tryptophanyl- and phenylalanyl-tRNA synthetases, respectively. In the serine/cysteine series, also selenocysteine is a proteinogenic amino acid that is inserted into proteins by a special translation mechanism, while the tellurocysteine is again most probably incorporated into proteins by the tolerance of the cysteinyl-tRNA synthetase. For research purposes, all of these natural and synthetic chalcogen amino acids have been extensively applied in peptide and protein research to exploit their different physicochemical properties for modulating structural and functional properties in synthetic peptides and rDNA expressed proteins as discussed in the following review

Cytosolic thioredoxin reductase 1 is required for correct disulfide formation in the ER

Folding of proteins entering the secretory pathway in mammalian cells frequently requires the insertion of disulfide bonds. Disulfide insertion can result in covalent linkages found in the native structure as well as those that are not, so‐called non‐native disulfides. The pathways for disulfide formation are well characterized, but our understanding of how non‐native disulfides are reduced so that the correct or native disulfides can form is poor. Here, we use a novel assay to demonstrate that the reduction in non‐native disulfides requires NADPH as the ultimate electron donor, and a robust cytosolic thioredoxin system, driven by thioredoxin reductase 1 (TrxR1 or TXNRD1). Inhibition of this reductive pathway prevents the correct folding and secretion of proteins that are known to form non‐native disulfides during their folding. Hence, we have shown for the first time that mammalian cells have a pathway for transferring reducing equivalents from the cytosol to the ER, which is required to ensure correct disulfide formation in proteins entering the secretory pathway

ERdj5 is the ER reductase that catalyzes the removal of non-native disulfides and correct folding of the LDL receptor

ERdj5 is a member of the protein disulfide isomerase family of proteins localized to the endoplasmic reticulum (ER) of mammalian cells. To date, only a limited number of substrates for ERdj5 are known. Here we identify a number of endogenous substrates that form mixed disulfides with ERdj5, greatly expanding its client repertoire. ERdj5 previously had been thought to exclusively reduce disulfides in proteins destined for dislocation to the cytosol for degradation. However, we demonstrate here that for one of the identified substrates, the low-density lipoprotein receptor (LDLR), ERdj5 is required not for degradation, but rather for efficient folding. Our results demonstrate that the crucial role of ERdj5 is to reduce non-native disulfides formed during productive folding and that this requirement is dependent on its interaction with BiP. Hence, ERdj5 acts as the ER reductase, both preparing misfolded proteins for degradation and catalyzing the folding of proteins that form obligatory non-native disulfides

Novel strategies for the synthesis of unsymmetrical glycosyl disulfides

yesNovel strategies for the efficient synthesis of unsymmetrical glycosyl disulfides are reported. Glycosyl disulfides are increasingly important as glycomimetics and molecular probes in glycobiology. Sialosyl disulfides are synthesised directly from the chlorosialoside Neu5Ac2Cl, proceeding via a thiol-disulfide exchange reaction between the sialosyl thiolate and symmetrical disulfides. This methodology was adapted and found to be successfully applicable to the synthesis of unsymmetrical glucosyl disulfides under mild conditions

Self-Assembled Monolayers of Symmetrical and Mixed Alkyl Fluoroalkyl Disulfides on Gold. 1. Synthesis of Disulfides and Investigation of Monolayer Properties

The synthesis of a variety of symmetrical bis(alkyl) and bis(fluoroalkyl) disulfides as well as mixed alkyl fluoroalkyl disulfides containing ester or amide groups is described. Self-assembled monolayers of these compounds on gold formed by spontaneous adsorption from solution are studied by contact angle measurements and polarized grazing incidence Fourier transform infrared spectroscopy (FTIR). The contact angles indicate tight packing of the molecules and the incorporation of both alkyl and fluoroalkyl chains in the monolayers. By means of FTIR, the typical tilted orientation of the alkyl chains is confirmed for monolayers derived from symmetrical alkyl disulfides, whereas, in self-assembled monolayers of the symmetrical fluorocarbon and the mixed disulfides, the molecules are oriented much closer to the surface normal direction. The wetting properties and the FTIR spectra of monolayers formed by coadsorption of an n-alkanethiol and a perfluorinated thiol are comparable to those formed by the self-assembly of the corresponding mixed disulfide. There is no indication for phase separation in any of the systems studied at room temperature. The mixed alkyl fluoroalkyl disulfides promise to form suitable monolayers on gold for the investigation of heat-induced phase separation on the gold surface

Inactivation of mammalian Ero 1α is catalysed by specific protein disulfide isomerases

Disulfide formation within the endoplasmic reticulum is a complex process requiring a disulfide exchange protein such as protein disulfide isomerase and a mechanism to form disulfides de novo. In mammalian cells, the major pathway for de novo disulfide formation involves the enzyme Ero1α which couples oxidation of thiols to the reduction of molecular oxygen to form hydrogen peroxide. Ero1α activity is tightly regulated by a mechanism that requires the formation of regulatory disulfides. These regulatory disulfides are reduced to activate and reform to inactive the enzyme. To investigate the mechanism of inactivation we analysed regulatory disulfide formation in the presence of various oxidants under controlled oxygen concentration. Neither molecular oxygen, nor hydrogen peroxide was able to oxidise Ero1α efficiently to form the correct regulatory disulfides. However, specific members of the PDI family such as PDI or ERp46 were able to catalyse this process. Further studies showed that both active sites of PDI contribute to the formation of regulatory disulfides in Ero1α and that the PDI substrate binding domain is crucial to allow electron transfer between the two enzymes. These results demonstrate a simple feedback mechanism of regulation of mammalian Ero1α involving its primary substrate