Comparison of metal-binding strength between methionine and cysteine residues: Implications for the design of metal-binding motifs in proteins

Self-contacting Cys, Ser, and Thr residues in high-resolution protein crystal structures: Tertiary constraints or hydrogen bonds?

Functional groups in the side-chains of at least 10 amino acids are mainly involved in tertiary interactions. However, structural and functional significance of intra-residue interactions has not been fully recognized. In this study, we have analyzed ~5800 non-redundant high-resolution protein structures and identified 1166 self-contacts between the side-chain S-H/O-H and backbone C=O groups in Cys, Ser, and Thr residues that satisfied the geometric criteria to form hydrogen bonds. Quantum chemical calculations using model compounds were used to evaluate single point energy for 45 representative examples from different allowed regions of Ramachandran map. Relative energy profiles obtained by varying the side-chain dihedral angle χ1 revealed that the energy difference between the crystal structure and the minimum energy conformations is between 0 and 3 kcal/mol. Natural bond orbital analysis (NBO) of self-contacting Cys residues revealed no charge transfer between Cys side-chain S-H and the backbone C=O groups. However, side-chain hydroxyl and the backbone C=O groups of 90%-95% of all self-contacting Ser and Thr residues are involved in charge transfer and the second order perturbation energy of majority of them is above 1 kcal/mol. Interaction energies calculated for model compounds along with NBO and NCIPLOT analyses demonstrate that the self-contacts observed in Ser and Thr residues can be described as hydrogen bonds. These interactions may provide stability to the loop/coil conformations. Self-contacting Cys residues are buried and the self-contacts appear to be mostly due to tertiary constraints. Dispersion between the self-contacting groups is one way to explain the close approach in Cys residues. Mutation studies will further validate and reveal the structural and functional significance of these self-contacting residues.

Identification and characterization of a rice expansin-like protein with metal-binding properties

Heavy metal (HM) contamination poses significant threat to agricultural productivity. This study identified and characterized Os09g29690 (OsELP), a rice expansin-like protein. We demonstrated OsELP localizes to the cell wall and is upregulated under various abiotic stresses. Sequence analysis revealed a potential metal-binding CXXXC motif in its conserved domain. Heterologous expression of OsELP in yeast mutants (Δacr3 and Δycf1) enhanced metal tolerance under arsenate [As(V)], arsenite [As(III)], and cadmium [Cd] stress. Yeast cells expressing OsELP accumulated higher amounts of As and Cd, suggesting a potential metal-binding mechanism. This was confirmed through site-directed mutagenesis on the conserved cysteine and serine residues within OsELP. Mutants lacking cysteine residues (mutCS) reduced tolerance to As(III) and Cd but enhanced tolerance to As(V), indicating a role of cysteine in As(III) and Cd binding. Conversely, mutants lacking serine residues (mutSA) reduced tolerance to As(V), suggesting serine's involvement in As(V) binding. These findings reveal the roles of cysteine and serine residues in mediating HM tolerance and binding, confirming OsELP as a key player in HM detoxification through cell wall localization and chelation. This study provides novel insights into the molecular mechanisms of HM tolerance in plants, with potential applications in developing crops with enhanced resistance to HM toxicity.

Gene-guided identifications of a structure-chimeric cyclotide viphi I from Viola philippica: Potential functions against cadmium and nematodes

The cyclic peptides, cyclotides, are identified mostly with 29-31-aa (amino acid residues) but rarely with ≥ 34-aa in plants. Viola philippica is a well-known medicinal plant but a rare metallophyte with cyclotides. A hypothesis was hence raised that the potential novel 34-aa cyclotide of Viola philippica would clearly broaden the structural and functional diversities of plant cyclotides. After homology-cloning the cyclotide precursor gene of VpCP5, a 34-aa cyclotide (viphi I) was identified to be larger than 22 other known cyclotides in V. philippica. It had a chimeric primary structure, due to its unusual loop structures (8 residues in loop 2 and 6 residues in loop 5) and aa composition (3 E and 5 R), by using phylogenetic analyses and an in-house cyclotide analysis tool, CyExcel_V1. A plasmid pCYC-viphi_I and a lab-used recombinant process were specially constructed for preparing viphi I. Typically, 0.12 or 0.25 mg ml-1 co-exposed viphi I could significantly remain cell activities with elevating Cd2+-exposed doses from 10-8 to 10-6 mol l-1 in MCF7 cells. In the model nematode Caenorhabditis elegans, IC50 values of viphi I to inhibit adult ratios and to induce death ratios, were 184.7 and 585.9 µg ml-1, respectively; the median lifespan of adult worms decreased from 14 to 2 d at viphi I doses ranging from 0.05 to 2 mg ml-1. Taken together, the newly identified viphi I exhibits functional potentials against cadmium and nematodes, providing new insights into structural and functional diversity of chimeric cyclotides in plants.

A Vitamin B2 -Photocatalysed Approach to Methionine Analogues

Access to new non-canonical amino acid residues is crucial for medicinal chemistry and chemical biology. Analogues of the amino acid methionine have been far less explored-despite their use in biochemistry, pharmacology and peptide bioconjugation. This is largely due to limited synthetic access. Herein, we exploit a new disconnection to access non-natural methionines through the development of a photochemical method for the radical α-C-H functionalization of sulfides with alkenes, in water, using inexpensive and commercially-available riboflavin (vitamin B2 ) as a photocatalyst. Our photochemical conditions allow the two-step synthesis of novel methionine analogues-by radical addition to unsaturated amino acid derivatives-and the chemoselective modification of peptide side-chains to yield non-natural methionine residues within small peptides. The mechanism of the bio-inspired flavin photocatalysis has been probed by experimental, DFT and TDDFT studies.

A Vitamin B2-Photocatalysed Approach to Methionine Analogues

Access to new non-canonical amino acid residues is crucial for medicinal chemistry and chemical biology. Analogues of the amino acid methionine have been far less explored-despite their use in biochemistry, pharmacology and peptide bioconjugation. This is largely due to limited synthetic access. Herein, we exploit a new disconnection to access non-natural methionines through the development of a photochemical method for the radical α-C-H functionalization of sulfides with alkenes, in water, using inexpensive and commercially-available riboflavin (vitamin B2) as a photocatalyst. Our photochemical conditions allow the two-step synthesis of novel methionine analogues-by radical addition to unsaturated amino acid derivatives-and the chemoselective modification of peptide side-chains to yield non-natural methionine residues within small peptides. The mechanism of the bio-inspired flavin photocatalysis has been probed by experimental, DFT and TDDFT studies.

Did Homocysteine Take Part in the Start of the Synthesis of Peptides on the Early Earth?

Unlike its shorter analog, cysteine, and its methylated derivative, methionine, homocysteine is not today a proteinogenic amino acid. However, this thiol containing amino acid is capable of forming an activated species intramolecularly. Its thiolactone could have made it an interesting molecular building block at the origin of life on Earth. Here we study the cyclization of homocysteine in water and show theoretically and experimentally that in an acidic medium the proportion of thiolactone is significant. This thiolactone easily reacts with amino acids to form dipeptides. We envision that these reactions may help interpret why a methionine residue is introduced at the start of all protein synthesis.

Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.

Development of Cobalt-Binding Peptide Chelate from Human Serum Albumin: Cobalt-Binding Properties and Stability

Radioactive isotopes are used as drugs or contrast agents in the medical field after being conjugated with chelates such as DOTA, NOTA, DTPA, TETA, CyDTA, TRITA, and DPDP. The N-terminal sequence of human serum albumin (HSA) is known as a metal binding site, such as for Co2+, Cu2+, and Ni2+. For this study, we designed and synthesized wAlb12 peptide from the N-terminal region of HSA, which can bind to cobalt, to develop a peptide-based chelate. The wAlb12 with a random coil structure tightly binds to the Co(II) ion. Moreover, the binding property of wAlb12 toward Co(II) was confirmed using various spectroscopic experiments. To identify the binding site of wAlb12, the analogs were synthesized by alanine scanning mutagenesis. Among them, H3A and Ac-wAlb12 did not bind to Co(II). The analysis of the binding regions confirmed that the His3 and α-amino group of the N-terminal region are important for Co(II) binding. The wAlb12 bound to Co(II) with Kd of 75 μM determined by isothermal titration calorimetry when analyzed by a single-site binding model. For the use of wAlb12 as a chelate in humans, its cytotoxicity and stability were investigated. Trypsin stability showed that the wAlb12 - Co(II) complex was more stable than wAlb12 alone. Furthermore, the cell viability analysis showed wAlb12 and wAlb12 + Co(II) to be non-toxic to the Raw 264.7 and HEK 293T cell lines. Therefore, a hot radioactive isotope such as cobalt-57 will have the same effect as a stable isotope cobalt. Accordingly, we expect wAlb12 to be used as a peptide chelate that binds with radioactive isotopes.

Molecular basis for lipid recognition by the prostaglandin D2 receptor CRTH2

Prostaglandin D₂ (PGD₂) signals through the G protein-coupled receptor (GPCR) CRTH2 to mediate various inflammatory responses. CRTH2 is the only member of the prostanoid receptor family that is phylogenetically distant from others, implying a nonconserved mechanism of lipid action on CRTH2. Here, we report a crystal structure of human CRTH2 bound to a PGD₂ derivative, 15R-methyl-PGD₂ (15mPGD₂), by serial femtosecond crystallography. The structure revealed a "polar group in"-binding mode of 15mPGD₂ contrasting the "polar group out"-binding mode of PGE₂ in its receptor EP3. Structural comparison analysis suggested that these two lipid-binding modes, associated with distinct charge distributions of ligand-binding pockets, may apply to other lipid GPCRs. Molecular dynamics simulations together with mutagenesis studies also identified charged residues at the ligand entry port that function to capture lipid ligands of CRTH2 from the lipid bilayer. Together, our studies suggest critical roles of charge environment in lipid recognition by GPCRs.

Sulfur Amino Acids: From Prebiotic Chemistry to Biology and Vice Versa

Two sulfur-containing amino acids are included in the list of the 20 classical protein amino acids. A methionine residue is introduced at the start of the synthesis of all current proteins. Cysteine, thanks to its thiol function, plays an essential role in a very large number of catalytic sites. Here we present what is known about the prebiotic synthesis of these two amino acids and homocysteine, and we discuss their introduction into primitive peptides and more elaborate proteins.

1 Introduction

2 Sulfur Sources

3 Prebiotic Synthesis of Cysteine

4 Prebiotic Synthesis of Methionine

5 Homocysteine and Its Thiolactone

6 Methionine and Cystine in Proteins

7 Prebiotic Scenarios Using Sulfur Amino Acids

8 Introduction of Cys and Met in the Genetic Code

9 Conclusion

Exploring human porphobilinogen synthase metalloprotein by quantum biochemistry and evolutionary methods

Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular interaction of zinc with the active center of the enzyme is unknown. In particular, quantum chemistry techniques within the density functional theory (DFT) framework have been the key methodology to describe metalloproteins, when one is looking for a compromise between accuracy and computational feasibility. Considering this, we used DFT-based models within the molecular fractionation with conjugate caps scheme to evaluate the binding energy features of zinc interacting with the human PBGS. Besides, phylogenetic and clustering analyses were successfully employed in extracting useful information from protein sequences to identify groups of conserved residues that build the ions-binding site. Our results also report a conservative assessment of the relevant amino acids, as well as the benchmark analysis of the calculation models used. The most relevant intermolecular interactions in Zn2+-PBGS are due to the amino acids CYS0122, CYS0124, CYS0132, ASP0169, SER0168, ARG0221, HIS0131, ASP0120, GLY0133, VAL0121, ARG0209, and ARG0174. Among these residues, we highlighted ASP0120, GLY0133, HIS0131, SER0168, and ARG0209 by co-occurring in all clusters generated by unsupervised clustering analysis. On the other hand, the triple cysteines at 2.5 Å from zinc (CYS0122, CYS0124, and CYS0132) have the highest energy attraction and are absent in the taxa Viridiplantae, Sar, Rhodophyta, and some Bacteria. Additionally, the performance of the DFT-based models shows that the processing time-dependence is more associated with the choice of the basis set than the exchange-correlation functional.

Does dilute nitric acid improve the removal of exogenous heavy metals from feathers? A comparative study towards the optimization of the cleaning procedure of feather samples prior to metal analysis

Feather analysis has been widely used as a biomonitoring tool to assess metal contamination in birds, as their sampling is a non-destructive and ethically preferable technique. However, for feathers to be useful as a biomonitor of heavy metals, exogenous contamination has to be efficiently removed. Although much effort has been put into this, no washing procedure has yet proven able to ensure the total removal of the surface-associated metals. The purpose of this study was to propose an efficient washing procedure of feather samples prior to metal analysis, on the basis of comparison of various washing schemes designed according to previous analytical trials, and of the verification of the efficacy of the optimal scheme in cleaning intentionally contaminated feathers. Our investigation showed that dilute nitric acid alone or in combination with a detergent (Extran) or acetone under mild agitation of the samples performed better that any other cleaning scheme applied. Thus, a multi-step procedure including the sequential use of all three reagents was tested against feather samples contaminated by adsorbed or particulate metal species. The procedure was able to completely eliminate the external metal loads in all cases except for the partial removal of severe contamination with adsorbed Cd.

A Novel Legionella Genomic Island Encodes a Copper-Responsive Regulatory System and a Single Icm/Dot Effector Protein Transcriptionally Activated by Copper

Legionella pneumophila is an intracellular human pathogen that utilizes amoebae as its environmental host. The adaptation of L. pneumophila to the intracellular environment requires coordination of expression of its multicomponent pathogenesis system, which is composed of a secretion system and effector proteins. However, the regulatory factors controlling the expression of this pathogenesis system are only partially uncovered. Here, we discovered a novel regulatory system that is activated by copper and controls the expression of a single effector protein. The genes encoding both the regulatory system and the effector protein are located on a genomic island that undergoes horizontal gene transfer within the Legionella genus. This regulator-effector genomic island represents the first reported case of local regulation of effectors in Legionella. The discovery of this regulatory mechanism is an important step forward in the understanding of how the regulatory network of effectors functions and evolves in the Legionella genus.

The intracellular pathogen Legionella pneumophila utilizes the Icm/Dot type IV secretion system to translocate >300 effector proteins into host cells during infection. The regulation of some of these effector-encoding genes was previously shown to be coordinated by several global regulators, including three two-component systems (TCSs) found in all the Legionella species examined. Here, we describe the first Legionella genomic island encoding a single Icm/Dot effector and a dedicated TCS, which regulates its expression. This genomic island, which we named Lci, undergoes horizontal gene transfer in the Legionella genus, and the TCS encoded from this island (LciRS) is homologous to TCSs that control the expression of various metal resistance systems found in other bacteria. We found that the L. pneumophila sensor histidine kinase LciS is specifically activated by copper via a unique, small periplasmic sensing domain. Upon activation by LciS, the response regulator LciR directly binds to a conserved regulatory element and activates the expression of the adjacently located lciE effector-encoding gene. Thus, LciR represents the first local regulator of effectors identified in L. pneumophila. Moreover, we found that the expression of the lciRS operon is repressed by the Fis1 and Fis3 regulators, leading to Fis-mediated effects on copper induction of LciE and silencing of the expression of this genomic island in the absence of copper. This island represents a novel type of effector regulation in Legionella, shedding new light on the ways by which the Legionella pathogenesis system evolves its effector repertoire and expands its activating signals.

Enhancement of erythritol production by Trichosporonoides oedocephalis ATCC 16958 through regulating key enzyme activity and the NADPH/NADP ratio with metal ion supplementation

Erythritol, a well-known natural sweetener, is mainly produced by microbial fermentation. Various metal ions (Al³⁺, Cu²⁺, Mn²⁺, and Ni²⁺) were added to the culture medium of Trichosporonoides oedocephalis ATCC 16958 at 30 mg/L in shake flask cultures. Compared with controls, Cu²⁺ increased the erythritol content by 86% and decreased the glycerol by-product by 31%. After 48 hr of shake flask culture, sodium dodecyl sulfate polyacrylamide gel electrophoresis showed that expression levels of erythrose reductase (ER) in the presence of 30 mg/L CuSO₄ · 5H₂O were higher than those obtained after treatment with other examined metal ions. Furthermore, after 108 hr of batch culture in a 5-L bioreactor, supplementation with 30 mg/L of CuSO₄ · 5H₂O increased the specific erythritol content by 27%. Further studies demonstrated that ER activity under 30 mg/L CuSO₄ · 5H₂O supplementation in a fermentor was overtly increased compared with the control after 60 hr, while glycerol-3-phosphate dehydrogenase activity was clearly reduced in most of the fermentation process. Furthermore, the NADPH/NADP ratio was slightly lower in T. oedocephalis cells treated with Cu²⁺ compared with control cells. These results provide further insights into Cu²⁺ effects on erythritol biosynthesis in T. oedocephalis and should improve the industrial production of erythritol by biological processes.