Cysteine Peptides Research Articles

Oral administration of cysteine peptides attenuates UV-B-induced skin erythema and pigmentation in humans

The oral administration of antioxidants may suppress UV-B-induced skin damage. HITHION YH-15, the extract of Torula yeast (Cyberlindnera jadinii), is rich in cysteine-containing peptides such as reduced and oxidized glutathione (GSH and GSSG), γ-glutamylcysteine (γ-Glu-Cys), and cysteinylglycine (Cys-Gly). These four constituents are termed cysteine peptides. In this study, we investigated the protective effects of cysteine peptides against UV-B in a randomized, placebo-controlled, double-blind, parallel-group study. A total of 90 healthy males and females aged 30–59 years were enrolled and randomized into two groups of 45 individuals each (cysteine peptides (48 mg/day) and placebo). Changes in UV-B-induced erythema and pigmentation were compared between groups after 5 weeks of test food intake. The minimal erythema dose (MED) significantly increased (*p = 0.019) in the cysteine peptides group compared to that in the placebo group, indicating suppression of UV-B-induced erythema. ΔL* value significantly increased (***p < 0.0001) in the cysteine peptides group compared to that in the placebo, indicating pigmentation suppression. We demonstrated that oral administration of cysteine peptides suppresses UV-B-induced erythema and pigmentation through multiple mechanisms. Thus, cysteine peptides may find use as nutricosmetics for maintaining skin health and well-being.UMIN Clinical Trials Registry ID: UMIN 000050157.

Identifying Quinones in Complex Aqueous Environmental Media (Biochar Extracts) through Tagging with Cysteine and Cysteine-Contained Peptides and High Resolution Mass Spectrometry Analysis.

Quinones are among the most important components in natural organic matter (NOM) for redox reactions; however, no quinones in complex environmental media have been identified. To aid the identification of quinone-containing molecules in ultracomplex environmental samples, we developed a chemical tagging method that makes use of a Michael addition reaction between quinones and thiols (-SH) in cysteine (Cys) and cysteine-contained peptides (CCP). After the tagging, candidates of quinones in representative aqueous environmental samples (water extractions of biochar) were identified through high-resolution mass spectrometry (HRMS) analysis. The MS and UV spectra analysis showed rapid reactions between Cys/CCP and model quinones with β-carbon from the same benzene ring available for Michael addition. The tagging efficiency was not influenced by other co-occurring nonquinone representative compounds, including caffeic acid, cinnamic acid, and coumaric acid. Cys and CCP were used to tag quinones in water extractions of biochars, and possible candidates of quinones (20 and 53 based on tagging with Cys and CCP, respectively) were identified based on the HRMS features for products of reactions with Cys/CCP. This study has successfully demonstrated that such a Michael addition reaction can be used to tag quinones in complex environmental media and potentially determine their identities. The method will enable an in-depth understanding of the redox chemistry of NOM and its critical chemical compositions and structures.

Insights into the production and evolution of lantibiotics from a computational analysis of peptides associated with the lanthipeptide cyclase domain.

Lanthipeptides are a large group of ribosomally encoded peptides cyclized by thioether and methylene bridges, which include the lantibiotics, lanthipeptides with antimicrobial activity. There are over 100 experimentally characterized lanthipeptides, with at least 25 distinct cyclization bridging patterns. We set out to understand the evolutionary dynamics and diversity of lanthipeptides. We identified 977 peptides in 2785 bacterial genomes from short open-reading frames encoding lanthipeptide modifiable amino acids (C, S and T) that lay chromosomally adjacent to genes encoding proteins containing the cyclase domain. These appeared to be synthesized by both known and novel enzymatic combinations. Our predictor of bridging topology suggested 36 novel-predicted topologies, including a single-cysteine topology seen in 179 lanthionine or labionin containing peptides, which were enriched for histidine. Evidence that supported the relevance of the single-cysteine containing lanthipeptide precursors included the presence of the labionin motif among single cysteine peptides that clustered with labionin-associated synthetase domains, and the leader features of experimentally defined lanthipeptides that were shared with single cysteine predictions. Evolutionary rate variation among peptide subfamilies suggests that selection pressures for functional change differ among subfamilies. Lanthipeptides that have recently evolved specific novel features may represent a richer source of potential novel antimicrobials, since their target species may have had less time to evolve resistance.

Selective Peptide Cysteine Manipulation on Demand and Difficult Protein Chemical Synthesis Enabled by Controllable Acidolysis of N,S-Benzylidene Thioacetals.

Although solid-phase peptide synthesis combining with chemical ligation provides a way to build up customized polypeptides in general, many targets are still presenting challenges for the conventional synthetic process, such as hydrophobic proteins. New methods and strategies are still required to overcome these obstacles. In this study, kinetic studies of Cys/Pen ligation and its acidolysis were performed, from which the fast acidolysis of substituted N,S-benzylidene thioacetals (NBTs) was discovered. The study demonstrates the potential of NBTs as a promising Cys switchable protection, facilitating the chemical synthesis of peptides and proteins by efficiently disrupting peptide aggregation. The compatibility of NBTs with other commonly adopted Cys protecting groups and their applications in sequential disulfide bond formation were also investigated. The first chemical synthesis of the native human programmed death ligand 1 immunoglobulin V-like (PD-L1 IgV) domain was achieved using the NBT strategy, showcasing its potential in difficult protein synthesis.

Selective Peptide Cysteine Manipulation on Demand and Difficult Protein Chemical Synthesis Enabled by Controllable Acidolysis of N,S‐Benzylidene Thioacetals

AbstractAlthough solid‐phase peptide synthesis combining with chemical ligation provides a way to build up customized polypeptides in general, many targets are still presenting challenges for the conventional synthetic process, such as hydrophobic proteins. New methods and strategies are still required to overcome these obstacles. In this study, kinetic studies of Cys/Pen ligation and its acidolysis were performed, from which the fast acidolysis of substituted N,S‐benzylidene thioacetals (NBTs) was discovered. The study demonstrates the potential of NBTs as a promising Cys switchable protection, facilitating the chemical synthesis of peptides and proteins by efficiently disrupting peptide aggregation. The compatibility of NBTs with other commonly adopted Cys protecting groups and their applications in sequential disulfide bond formation were also investigated. The first chemical synthesis of the native human programmed death ligand 1 immunoglobulin V‐like (PD‐L1 IgV) domain was achieved using the NBT strategy, showcasing its potential in difficult protein synthesis.

NCF4 regulates antigen presentation of cysteine peptides by intracellular oxidative response and restricts activation of autoreactive and arthritogenic T cells

Autoimmune diseases, such as rheumatoid arthritis (RA) and systemic lupus erythematous, are regulated by polymorphisms in genes contributing to the NOX2 complex. Mutations in both Ncf1 and Ncf4 affect development of arthritis in experimental models of RA, but the different regulatory pathways mediated by NOX2-derived reactive oxygen species (ROS) have not yet been clarified.Here we address the possibility that intracellular ROS, regulated by the NCF4 protein (earlier often denoted p40phox) which interacts with endosomal membranes, could play an important role in the oxidation of cysteine peptides in mononuclear phagocytic cells, thereby regulating antigen presentation and activation of arthritogenic T cells.To study the role of NCF4 we used mice with an amino acid replacing mutation (NCF4R58A), which is known to affect interaction with endosomal membranes, leading to decreased intracellular ROS production. To study the impact of NCF4 on T cell activation, we used the glucose phosphate isomerase peptide GPI325-339, which contains two cysteine residues (325-339c-c). Macrophages from mice with the NCF458A mutation efficiently presented the peptide when the two cysteines were intact and not crosslinked, leading to a strong arthritogenic T cell response. T cell priming occurred in the draining lymph nodes (LNs) within 8 days after immunization. Clodronate treatment, which depletes antigen-presenting mononuclear phagocytes, ameliorated arthritis severity, whereas treatment with FYT720, which traps activated T cells in LNs, prohibited arthritis.We conclude that NCF4-dependent intracellular ROS maintains cysteine peptides in an oxidized crosslinked state, which prevents presentation of peptides recognized by non-tolerized T cells and thereby protects against autoimmune arthritis.

A150 DEVELOPMENT OF MIMETIC MATRICES AS INSTRUCTIVE ORGANOIDS MICROENVIRONMENT FOR THE STUDY OF COLONIC DISEASES

Abstract Background The functional complexity of the colonic epithelium is dependent on its interaction with the microenvironment involving gradients of soluble factors, extracellular matrix (ECM) proteins and stiffness. The influence of dynamic changes in the ECM has been observed in tumours, with variations in protein expression and rigidity. Their biomolecular impacts on epithelial cell behaviour are less studied due to the structural complexity of the matrix. Organoids offers a novel approach for the study of ECM biodynamics, as they require a matrix (Matrigel) to develop. Previous work showed that it is possible to grow organoids in hydrogels other than Matrigel. To evaluate the effect of matrix composition alteration on cancer initiation, we developed biofunctionalized composite hydrogels that mimic the ECM changes (chemical and physical) observed in the BmpR1a-deficient telocytes Foxl1 + (Bmpr1a△Foxl1+) mouse model of colorectal cancer (CRC) initiation. Aims The development of mimetic matrices, in association with organoids, would enable us to uncover the impact of matrix deregulation on colonic cells behaviour in pathogenesis process. Methods These hydrogels were made of alginate and 8-arm polyethylene glycol- vinyl sulfone (PEG) macromers bearing cysteine residues (CYS) and peptides. Four peptides derived from fibronectin, laminin 111, collagen I and collagen IV were used to mimic the ECM changes in the Bmpr1a△Foxl1+ colon. The grafting of CYS on alginate or peptides on PEG macromers was first characterized by thiol quantification assays. The non-grafted peptides were also analysed by uHPLC. Stiffness of the hydrogels was then determined by dynamic mechanical analysis. Finally, normal mouse organoids were seeded on hydrogels and evaluated for survival by live/dead labeling and proliferation by Alamar blue assays. Matrigel was used as a control. Results Chemical characterization revealed that CYS were grafted onto the alginate chain at around 190 μmol/g alginate. The PEG macromers were functionalized with four peptides at concentration varying from 0.25 to 1.5 mM. Rigidity of the hydrogels depends on the concentration of alginate used where lower concentration leads to soft matrix (0.5 kPa, homeostasis) and high concentration produced a stiff matrix (4 kPa, diseased). Organoids seeded in these mimetic composite hydrogels survived and proliferated in comparison to alginate alone. Conclusions Our results indicate that we can develop mimetic composite hydrogels where colon organoids can survive and thrive. This is a breakthrough model for defining the roles of ECM mechanical and biochemical stimuli in epithelial behaviour during the initiation and development of CRC. Funding Agencies CIHR

Targeted siRNA delivery to lung epithelia reduces airway inflammation in a mouse model of allergic asthma

Asthma is a chronic inflammatory disease triggered by allergic reactions in the bronchia. These reactions lead to swelling of mucous membranes, hypersecretion of mucus, and bronchoconstriction, resulting in a restricted opening of the lung airway. Allergic pulmonary inflammation and airway hyperresponsiveness are induced when Th2 cytokines, such as interleukin (IL)-4 and IL-13, bind to their cognate receptors on lung epithelial cells. Specifically, IL-13 stimulates inflammation through a multi-subunit receptor, mainly the alpha chain of the IL-4 receptor (IL-4Rα), which also plays a role in IL-4 signaling. In this study, we employed a lung epithelial cell-targeting siRNA carrier composed of a rabies virus glycoprotein-derived small peptide coupled with cationic nona-arginine and trileucine before cysteine peptide (RVG9R3LC). This carrier was complexed with siRNA, enabling targeted delivery of therapeutic siRNA to IL-4Rα (siIL4Rα) expressed in lung epithelial cells within an asthma model in vivo. Our approach demonstrated efficient gene knockdown in cultured lung epithelial cells and in vivo. Furthermore, two administrations of therapeutic siIL4Rα protected the ovalbumin-sensitized and challenged asthma mouse model from airway inflammation and excessive mucus secretion. Our findings suggest that the peptide-siRNA carrier system presents a promising therapeutic approach for respiratory inflammation.Graphical abstract

Increasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data Acquisition.

Intelligent data acquisition (IDA) strategies, such as a real-time database search (RTS), have improved the depth of proteome coverage for experiments that utilize isobaric labels and gas phase purification techniques (i.e., SPS-MS3). In this work, we introduce inSeqAPI, an instrument application programing interface (iAPI) program that enables construction of novel data acquisition algorithms. First, we analyze biotinylated cysteine peptides from ABPP experiments to demonstrate that a real-time search method within inSeqAPI performs similarly to an equivalent vendor method. Then, we describe PairQuant, a method within inSeqAPI designed for the hyperplexing approach that utilizes protein-level isotopic labeling and peptide-level TMT labeling. PairQuant allows for TMT analysis of 36 conditions in a single sample and achieves ∼98% coverage of both peptide pair partners in a hyperplexed experiment as well as a 40% improvement in the number of quantified cysteine sites compared with non-RTS acquisition. We applied this method in the ABPP study of ligandable cysteine sites in the nucleus leading to an identification of additional druggable sites on protein- and DNA-interaction domains of transcription regulators and on nuclear ubiquitin ligases.

2-cyanopyridine derivatives enable N-terminal cysteine bioconjugation and peptide bond cleavage of glutathione under aqueous and mild conditions.

Inspired by the chemical reactivity of apalutamide, we have developed an efficient method for N-terminal cysteine bioconjugation with 2-cyanopyridine derivatives. Systematic investigations of various 2-cyanopyridines revealed that 2-cyanopyridines with electron-withdrawing groups react efficiently with cysteine under aqueous and mild conditions. Moreover, the highly reactive 2-cyanopyridines enable the peptide bond cleavage of glutathione. The utility of our method is demonstrated by its application to the cysteine-selective chemical modification of bioactive peptides.

Azole reagents enabled ligation of peptide acyl pyrazoles for chemical protein synthesis.

Native chemical ligation (NCL) has been playing an increasingly important role in chemical protein synthesis (CPS). More efficient ligation methods that circumvent the requirement of a peptidyl thioester and thiol additive-which allow the following desulfurization or refolding in one pot-are urgently needed for the synthesis of more complex protein targets and in large quantities. Herein, we discover that the weak acyl donor peptidyl N-acyl pyrazole can be activated by azole reagents like 3-methylpyrazole or imidazole to facilitate its ligation directly with an N-terminal cysteine peptide. As it requires no thioester or thiol additive, this ligation strategy can be conveniently combined with metal-free desulfurization (MFD) or oxidative protein folding to allow various one-pot protocols. The utility and generality of the strategy are showcased by the total synthesis of ubiquitin via an N-to-C sequential ligation-MFD strategy, the semi-synthesis of the copper protein azurin, and the efficient assembly of a sulfated hirudin variant and the cyclotide kalata B1, all in a one-pot fashion.

Synthetic Dual Cysteine-ADP Ribosylated Peptides from the Androgen Receptor are Recognized by the DTX3L/PARP9 Complex.

Androgen signaling in prostate cancer cells involves multisite cysteine ADP-ribosylation of the androgen receptor (AR) by PARP7. The AR modification is read by ADP-ribosyl binding macrodomains in PARP9, but the reason that multiple cysteines are modified is unknown. Here, we use synthetic peptides to show that dual ADP-ribosylation of closely spaced cysteines mediates recognition by the DTX3L/PARP9 complex. Mono and dual ADP-ribosylated cysteine peptides were prepared using a novel solid-phase synthetic strategy utilizing a key, Boc-protected, ribofuranosylcysteine building block. This synthetic strategy allowed us to synthesize fluorescently labeled peptides containing a dual ADP-ribosylation motif. It was found that the DTX3L/PARP9 complex recognizes the dual ADP-ribosylated AR peptide (Kd = 80.5 nM) with significantly higher affinity than peptides with a single ADP-ribose. Moreover, oligomerization of the DTX3L/PARP9 complex proved crucial for ADP-ribosyl-peptide interaction since a deletion mutant of the complex that prevents its oligomer formation dramatically reduced peptide binding. Our data show that features of the substrate modification and the reader contribute to the efficiency of the interaction and imply that multivalent interactions are important for AR-DTX3L/PARP9 assembly.

Lipopolysaccaride-binding peptides modified Au electrode for the sensitive detection of lipopolysaccharide in water

Lipopolysaccaride(LPS) is the main structural component of the outer membrane of Gram-negative bacteria and causes serious harm to people's health. Thus, in-time detection of LPS in environment is required. Herein, a new LPS electrochemical detection method was developed by using ferricenecarboxylic acid (FCA)-labeled LPS-binding peptide as biomolecular recognition element and electrochemical signal. Au nanoparticles were assembled on 1,6-hexanedithiol modified Au electrode through sulfhydryl groups, and FCA labeled the C-terminal cysteine of LPS-binding peptide was assembled on Au nanoparticles to achieve its immobilization on the electrode surface. In presence of hexaammineruthenium(II/III), a mediated process between ferricene and hexaammineruthenium(II) resulted in electrical signal amplification. The addition of LPS and the its binding with peptides will induce more hexaammineruthenium(III) to access electrode, resulting in the reduction peak current of the hexaammineruthenium(III) and oxidation peak current of ferrocene both increased. The increased electrochemical signals are used to indicate the concentration of LPS. As a result, a highly-sensitive electrochemical method was developed for the rapid determination of LPS. The linear range was from 1.25 to 30 pg mL−1, and the detection limit was 0.039 pg mL−1. It was used in detection of LPS in environmental water samples, and the results consisted with that obtained by Limulus method.

Development of a spectrophotometric method for assessment of the relative reactivity of monocarbonyl analogs of curcumin with 2-(dimethylamino)ethanethiol

In order to improve the bioavailability of curcumin, studies have been undertaken to prepare the so-called monocarbonyl analogs of curcumin (MACs) and assess their biological activity. These analogs contain an electrophilic α,β-unsaturated carbonyl moiety (Michael acceptor). Several key biological processes are connected/controlled with thiol alkylation (glutathione, cysteine, cysteine peptide residues). The most likely reaction is the Michael addition between the α,β-unsaturated acceptor and a corresponding thiol. 2,6-Bisarylidenecyclohexanone and 3,5-bisarylidenepiperidin-4-one scaffolds offer convenient tunability of electrophilicity and redox properties of the Michael acceptor by the introduction of various substituents. In this study, several MACs were prepared by Claisen-Schmidt condensation reaction, and their reactivity with 2-(dimethylamino)ethanethiol was evaluated. For this purpose, based on the UV-Vis spectra of the analogs and thiol(s), a proper method for spectrophotometric evaluation of their reactivity with 2-(dimethylamino)ethanethiol was optimized. The relative reactivity of the analogs was 7 &gt; 2 &gt; 5 &gt; 4 &gt; 1 ≈ 6. The developed method is simple, and it can be extended to assess the reactivity of other MACs.

Defining the reactivity of nanoparticles to peptides through direct peptide reactivity assay (DPRA) using a high pressure liquid chromatography system with a diode array detector.

The possibility of inducing skin sensitization reactions following exposure to various chemicals can lead to skin diseases, and the evaluation of skin sensitivity to such substances is very important. However, as animal tests for skin sensitization are prohibited, the OECD Test Guideline 442C was designated as part of an alternative testing method. Therefore, in this study, the reactivity of cysteine and lysine peptides to nanoparticle substrates was identified through HPLC-DAD analysis according to the skin sensitization animal replacement test method specified in the OECD Test Guideline 442C. In this study, all criteria for skin sensitization experiments specified in OECD Test Guideline 442C were satisfied. As a result of analyzing the disappearance rates of cysteine and lysine peptides for the five types of nanoparticle substrates (TiO2, CeO2, Co3O4, NiO, and Fe2O3) using the established analytical method, all were identified as positive. Therefore, our findings suggest that basic data from this technique can contribute to skin sensitization studies by providing the depletion percentage of cysteine and lysine peptides for nanoparticle materials that have not yet been tested for skin sensitization.

The Effect of Cysteine Peptide Ingestion on Skin Brightness, a Randomized, Double-Blind, Placebo-Controlled, Parallel-Group Human Clinical Trial

Glutathione (GSH) is present in almost all human cells and has a beneficial effect on human skin brightness. Cysteinylglycine (Cys-Gly) and γ-glutamylcysteine (γ-Glu-Cys) are GSH synthesis components. In this study, we defined glutathione (GSH), cysteinylglycine (Cys-Gly), and γ-glutamylcysteine (γ-Glu-Cys) as cysteine peptide and performed a randomized, double-blind, placebo-controlled study to investigate the effects of orally administered cysteine peptide on human skin brightness using a CM-26d portable spectrophotometer in healthy males and females aged between 20 and 65 years old. Eligible participants were randomly allocated into three groups (cysteine peptide 45 mg: n = 16, 90 mg: n = 15, and placebo: n = 16). Each subject ingested six tablets every day for 12 weeks, and skin brightness was measured at 0, 4, 8, and 12 weeks. As a result, the 45 mg group exhibited arm brightening in a time-dependent manner, and a significant difference was observed compared to the placebo at week 12 (p = 0.028). Moreover, no serious adverse events and changes related to 270 mg study food were observed in the safety trial. Here, we suggest that cysteine peptide is a promising and safe compound for human skin brightness.

LncRNA DANCR restrained the survival of mycobacterium tuberculosis H37Ra by sponging miR-1301-3p/miR-5194.

Tuberculosis is a worldwide contagion caused by Mycobacterium tuberculosis (MTB). MTB is characterized by intracellular parasitism and is semi-dormant inside host cells. The persistent inflammation caused by MTB can form a granuloma in lesion regions and intensify the latency of bacteria. In recent years, several studies have proven that long non-coding RNAs (lncRNAs) play critical roles in modulating autophagy. In our study, the Gene Expression Omnibus (GEO) databases were searched for lncRNAs that are associated with tuberculosis. We found that lncRNA differentiation antagonizing non-protein coding RNA (DANCR) increased in the peripheral blood samples collected from 54 pulmonary tuberculosis patients compared to 23 healthy donors. By constructing DANCR overexpression cells, we analyzed the possible cellular function of DANCR. After analyzing our experiments, it was found that the data revealed that upregulation of DANCR facilitated the expression of signal transducer and activator of transcription 3, autophagy-related 4D cysteine peptides, autophagy-related 5, Ras homolog enriched in the brain, and microtubule-associated protein 1A/1B light chain 3 (STAT3, ATG4D, ATG5, RHEB, and LC3, respectively) by sponging miR-1301-3p and miR-5194. Immunofluorescence analysis indicated that DANCR played a positive role in both autophagosome formation and fusion of autolysosomes in macrophages. The colony-forming unit (CFU) assay data also showed that the cells overexpressing DANCR were more efficient in eliminating the intracellular H37Ra strain. Consequently, these data suggest that DANCR restrained intracellular survival of M. tuberculosis by promoting autophagy via miR-1301-3p and miR-5194.

Development of a peptide reactivity assay for screening botanicals and natural substances: Proof of concept studies

Consumer products containing botanicals or natural substances (BNS) are often preferred because there is a perception that ‘natural’ is safe. As with any product ingredient, a thorough safety assessment must be conducted, including a determination of skin sensitization potential. A modification of the Peroxidase Peptide Reactivity Assay (PPRA) was explored for screening BNS (B-PPRA) for their reactivity to a model cysteine peptide. The PPRA incorporates a horseradish peroxidase‑hydrogen peroxide (+HRP/P) oxidation system for the activation of potential pre- and pro-haptens. BNS test materials contained <2% botanical constituent in either glycerin/water or propylene glycol/water. Stock solutions prepared in acetonitrile were diluted to 8 working concentrations. Direct reactivity was determined in reaction mixtures containing peptide and deferoxamine in potassium phosphate buffer. Enzyme-mediated reactivity determinations were performed with addition of +HRP/P. Initial studies demonstrated that results were reproducible and impact of carrier low. To determine the sensitivity of the assay, experiments were conducted with chamomile extract spiked with three sensitizers. Peptide depletion was observed in the +HRP/P reaction mixtures with isoeugenol spikes as low as 0.05%. The B-PPRA shows promise as a screening method for skin sensitization potential and could become part of a framework for the skin sensitization safety assessment of BNS.

Ferrihydrite synthesis in the presence of amino acids and artificial seawater.

Ferrihydrite is widespread in clays, soils, and living organisms and was found on Mars. This iron-mineral could be found on the prebiotic Earth, which also contained simple monomeric amino acids. For prebiotic chemistry, it is important to understand how amino acids have an effect on the process of iron oxide formations. There are three important results in this work: (a) preconcentration of cysteine and aspartic acid, (b) formation of cystine and probably the cysteine peptide occurred during ferrihydrite syntheses, and (c) amino acids have an effect on iron oxide synthesis. For samples containing aspartic acid and cysteine, their presence on the surface or mineral structure can be confirmed by FT-IR spectra. Surface charge analysis showed a relatively high decrease for samples synthesized with cysteine. Scanning electron microscopy did not show marked morphological differences among the samples, except for the seawater sample containing cysteine, which had a lamina-shaped morphology surrounded by circular iron particles, indicating the possible formation of a cysteine structure involving iron oxide particles. The thermogravimetric analysis of the samples indicates that the presence of salts and amino acids in the synthesis of ferrihydrite has an effect on the thermal behavior of the iron oxide/amino acids and modifying the water-loss temperature. The heating of the cysteine samples, synthesized in distilled water and artificial seawater, showed several peaks of degradation of cysteine. In addition, heating of the aspartic acid samples produced the polymerization of this amino acid and peaks of degradation of it. FTIR spectra and XRD patterns did not indicate the precipitation of methionine, 2-aminoisobutyric acid, lysine, or glycine with the iron oxide formations. However, the heating of the glycine, methionine and lysine samples, synthesized in artificial seawater, showed peaks that could be attributed to the degradation of them. Then this could be an indication that these amino acids precipitate with the minerals during the syntheses. Also, the dissolution of these amino acids in artificial seawater prevents the formation of ferrihydrite.

Thermodynamics and transport properties of valine and cysteine peptides in water

The study of thermodynamic and transport properties of amino acids gives access to knowledge about interactions between distinct molecules necessary to understand a variety of biological processes. In this work, we have performed molecular dynamics simulations of valine and cysteine peptides with lengths of (n) = 1, 2, 4, 8 & 16 monomers in an aqueous environment to estimate the solvation free energy and diffusion coefficients. We modeled our system using OPLS-AA parameter sets and TIP3P water at 310 K temperature. Solvation free energy of both the peptides have been reported using two thermodynamic integration (TI) based methods: TI and TI-CUBIC. The solvation free energy of both the peptides increases with the chain length. The estimated values using both methods are in good agreement with a statistical error of < 3%. The solvent accessible surface area (SASA) of solutes and hydrogen bonds between solute and solvent have also been presented to get more insights on solvation processes. The increase in solvation energy of both peptides with chain length is further corroborated by increase in the number of hydrogen bond (between peptide and water) and SASA with the chain length. In addition, the self diffusion coefficient of both solute and solvent along with their binary diffusion coefficient have been estimated for both the peptides. Furthermore, the effect of chain length on solvation free energy as well as diffusion coefficients have been studied.