Transient homodimer interactions studied using the electron self-exchange reaction

Dryopteris crassirhizoma Nakai.: A review of its botany, traditional use, phytochemistry, pharmacological activity, toxicology and pharmacokinetics

ETHNOPHARMACOLOGICAL RELEVANCE

The Dryopteris crassirhizoma Nakai., a commonly used herb, is known as "Guan Zhong" in China, "Oshida" in Japan and "Gwanjung" in Korea. It has long been used for parasitic infestation, hemorrhages and epidemic influenza.

AIM OF THE REVIEW

The present paper aims to provide an up-to-date review at the advancements of the investigations on the traditional use, phytochemistry, pharmacological activity, toxicology and pharmacokinetics of D. crassirhizoma. Besides, possible trends, therapeutic potentials, and perspectives for future research of this plant are also briefly discussed.

MATERIALS AND METHODS

Relevant information on traditional use, phytochemistry, pharmacological activity, toxicology and pharmacokinetics of D. crassirhizoma was collected through published materials and electronic databases, including the Chinese Pharmacopoeia, Flora of China, Web of Science, PubMed, Baidu Scholar, Google Scholar, and China National Knowledge Infrastructure. 109 papers included in the article and we determined that no major information was missing after many checks. All authors participated in the review process for this article and all research paper are from authoritative published materials and electronic databases.

RESULTS

130 chemical components, among which phloroglucinols are the predominant groups, have been isolated and identified from D. crassirhizoma. D. crassirhizoma with its bioactive compounds is possessed of extensive biological activities, including anti-parasite, anti-microbial, anti-viral, anti-cancer, anti-inflammatory, anti-oxidant, anti-diabetic, bone protective, immunomodulatory, anti-platelet and anti-hyperuricemia activity. Besides, D. crassirhizoma has special toxicology and pharmacokinetics characterization.

CONCLUSIONS

D. crassirhizoma is a traditional Chinese medicine having a long history of application. This review mainly summarized the different chemical components extract from D. crassirhizoma and various reported pharmacological effects. Besides, the toxicology and pharmacokinetics of D. crassirhizoma also be analysed in this review. However, the chemical components of D. crassirhizoma are understudied and require further research to expand its medicinal potential, and it is urgent to design a new extraction scheme, so that the active ingredients can be obtained at a lower cost.

Manipulating electron transfer – the influence of substituents on novel copper guanidine quinolinyl complexes

Copper guanidine quinolinyl complexes act as good entatic state models due to their distorted structures leading to a high similarity between Cu(i) and Cu(ii) complexes. For a better understanding of the entatic state principle regarding electron transfer a series of guanidine quinolinyl ligands with different substituents in the 2- and 4-position were synthesized to examine the influence on the electron transfer properties of the corresponding copper complexes. Substituents with different steric or electronic influences were chosen. The effects on the properties of the copper complexes were studied applying different experimental and theoretical methods. The molecular structures of the bis(chelate) copper complexes were examined in the solid state by single-crystal X-ray diffraction and in solution by X-ray absorption spectroscopy and density functional theory (DFT) calculations revealing a significant impact of the substituents on the complex structures. For a better insight natural bond orbital (NBO) calculations of the ligands and copper complexes were performed. The electron transfer was analysed by the determination of the electron self-exchange rates following Marcus theory. The obtained results were correlated with the results of the structural analysis of the complexes and of the NBO calculations. Nelsen's four-point method calculations give a deeper understanding of the thermodynamic properties of the electron transfer. These studies reveal a significant impact of the substituents on the properties of the copper complexes.

Copper guanidine quinolinyl complexes act as good entatic state models for the electron transfer due to a high similarity between the corresponding Cu(i) and Cu(ii) complexes. The introduction of substituents leads to a further enhancement.

New molecular packing in a crystal of pseudoazurin from Alcaligenes faecalis: a double-helical arrangement of blue copper

Pseudoazurin from the denitrifying bacterium Alcaligenes faecalis (AfPAz) is a blue copper protein and functions as an electron donor to copper-containing nitrite reductase (CuNIR). Conventionally, AfPAz has been crystallized using highly concentrated ammonium sulfate as a precipitant. Here, a needle-like crystal of AfPAz grown in a solution containing a macromolecular precipitant, polyethylene glycol 8000 (PEG 8000), is reported. The crystal belonged to space group P61, with unit-cell parameters a = b = 68.7, c = 94.2 Å. The structure has been determined and refined at 2.6 Å resolution. The asymmetric unit contained two AfPAz molecules contacting each other on negatively charged surfaces. The molecular packing of the crystal showed a right-handed double-helical arrangement of AfPAz molecules and hence of blue copper sites. This structure provides insight into the excluded-volume effect of PEG and the manner of assembly of AfPAz.

The ClusPro web server for protein-protein docking

The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.

Regulation of protein function: crystal packing interfaces and conformational dimerization

The accepted view of interprotein electron transport involves molecules diffusing between donor and acceptor redox sites. An emerging alternative hypothesis is that efficient long-range electron transport can be achieved through proteins arranged in supramolecular assemblies. In this study, we have investigated the crystal packing interfaces in three crystal forms of plastocyanin, an integral component of the photosynthetic electron transport chain, and discuss their potential relevance to in vivo supramolecular assemblies. Symmetry-related protein chains within these crystals have Cu-Cu separations of <25 A, a distance that readily supports electron transfer. In one structure, the plastocyanin molecule exists in two forms in which a backbone displacement coupled with side chain rearrangements enables the modulation of protein-protein interfaces.

The role of ligand-containing loops at copper sites in proteins

Many approaches are being used to engineer metalloproteins, with most of these informed by, and aiming to further elucidate, the basic structural requirements for biological metal centers. Cupredoxins are type 1 (T1) copper-containing electron transfer (ET) proteins with a -barrel fold that is thought to constrain metal site structure. The T1 copper ion is bound by ligands mainly originating from a single active site loop whose length and structure varies. This Highlight article will focus on protein engineering studies which have investigated the role of the metal-binding loop for active site integrity and functionality. Scaffold differences are present within the cupredoxin family and their influence has also been assessed. Given the widespread occurrence of -barrel domains in nature, and the array of metal sites in proteins composed of loop regions, the studies described on this model system have implications for a variety of metalloproteins.

Modulation of heme redox potential in the cytochrome c6 family

Cytochrome c6A is a unique dithio-cytochrome of green algae and plants. It has a very similar core structure to that of bacterial and algal cytochromes c6 but is unable to fulfill the same function of transferring electrons from cytochrome f to photosystem I. A key feature is that its heme midpoint potential is more than 200 mV below that of cytochrome c6 despite having His and Met as axial heme-iron ligands. To identify the molecular origins of the difference in potential, the structure of cytochrome c6 from the cyanobacterium Phormidium laminosum has been determined by X-ray crystallography and compared with the known structure of cytochrome c6A. One salient difference of the heme pockets is that a highly conserved Gln (Q51) in cytochrome c6 is replaced by Val (V52) in c6A. Using protein film voltammetry, we found that swapping these residues raised the c6A potential by +109 mV and decreased that of c6 by almost the same extent, -100 mV. X-ray crystallography of the V52Q protein showed that the Gln residue adopts the same configuration relative to the heme as in cytochrome c6 and we propose that this stereochemistry destabilizes the oxidized form of the heme. Consequently, replacement of Gln by Val was probably a key step in the evolution of cytochrome c6A from cytochrome c6, inhibiting reduction by the cytochrome b6f complex and facilitating establishment of a new function.

Ligand and loop variations at type 1 copper sites: influence on structure and reactivity

Type 1 (T1) copper sites promote biological electron transfer and are found in the cupredoxins and a number of copper-containing enzymes including the multi-copper oxidases. A T1 copper site usually has a distorted tetrahedral geometry with strong ligands provided by the thiolate sulfur of a Cys and the imidazole nitrogens of two His residues. The active site structure is typically completed by a weak axial Met ligand (a second weak axial interaction is found in azurin resulting in a trigonal bipyramidal geometry). The axial Met is not conserved and Gln, Phe, Leu and Val are also found in this position. Three of the four ligands at a T1 copper site are situated on a single C-terminal loop whose length and structure varies. Studies are discussed which investigate both the influence of physiologically relevant axial ligand alterations, and also of mutations to the length and structure of the ligand-containing loop, on the properties of T1 copper sites.