Natural Amino Acids Research Articles

Synthesis of Gold Nanosheets with Controlled Morphology by Combining a Natural Amino Acid with High-Frequency Ultrasound

Synthesis of Gold Nanosheets with Controlled Morphology by Combining a Natural Amino Acid with High-Frequency Ultrasound

Transcriptome Analysis Reveals the Molecular Mechanism of GABA Accumulation during Quinoa (Chenopodium quinoa Willd.) Germination.

Quinoa (Chenopodium quinoa Willd.) with a history of 5000 years as food is extremely rich in nutrients and bioactive compounds, including γ-aminobutyric acid (GABA), a natural four-carbon non-protein amino acid with great benefits to human health. In quinoa, GABA generally increases with the germination time, but the underlying molecular mechanism is unclear. Here, we found that the GABA content in quinoa varied significantly among 25 varieties using an automatic amino acid analyzer. Next, six varieties (three low-GABA and three high-GABA varieties) were used for further analyses. The content of GABA in six varieties all showed an increasing trend after germination. In addition, Pearson's correlation analysis showed that the changes in GABA content were closely related to the transcript level or enzyme activity of three key enzymes including glutamate decarboxylase (GAD), GABA transaminase (GABA-T), and succinate-semialdehyde dehydrogenase (SSADH) in the GABA shunt, especially GAD. Based on RNA-sequencing analysis, eight GAD genes, two GABA-T genes, one SSADH gene, nine polyamine oxidase (PAO) genes, five diamine oxidase (DAO) genes, four 4-aminobutyraldehyde dehydrogenase (BADH) genes, and three thermospermine synthase ACAULIS5 (ACL5) genes were identified. Among these, CqGAD8 and CqGABA-T2 may make a greater contribution to GABA accumulation during quinoa germination.

Вплив L-орнітину-L-аспартату на деякі показники функції печінки в пацієнтів після резекції печінки

У статті розглянуто питання впливу L-орнітину-L-аспартату (Гепа-Мерц) на білок­синтезуючу функцію печінки при її резекції з приводу первинного або метастатичного ураження. L-орнітин-L-аспартат — сіль природних амінокислот орнітину та аспартату, що покращують виживання гепатоцитів, збільшують їх кількість і вірогідно посилюють секрецію ними трансферину in vitro. На базі відділення анестезіології та інтенсивної терапії Національного інституту раку (м. Київ) проведено проспективне дослідження ефективності L-орнітину-L-аспартату при його використанні в онкологічних хворих у періопераційному періоді, яким були охоплені 42 пацієнти, прооперовані під загальним інгаляційним наркозом у комбінації з продовженою епідуральною анестезією, які були розподілені на дві групи. Хворі 1-ї групи отримували внутрішньовенно L-орнітин-L-аспартат (Гепа-Мерц) у дозі 10 мл (5 г) 1 раз на добу за 2 доби до і впродовж 3–4 днів після операції, хворим контрольної групи L-орнітин-L-аспартат не призначали. Показано, що періопераційне введення L-орнітину-L-аспартату у хворих із резекцією печінки може позитивно впливати на показники ефективності синтетичної функції печінки.

Development and Characterization of Light-Responsive Peptide Macrocycles.

Small molecules, peptide macrocycles, and protein conjugates that reversibly turn their function on and off in response to visible light enabled the fields of photopharmacology and optochemical genetics. In this chapter, we describe a method for the synthesis of light-responsive (LR) macrocycles from linear peptides composed of 20 natural amino acids. Bioactive LR molecules can be produced by grafting azobenzene or other LR-structures onto molecules with known biological functions (e.g., alpha-helical peptides). The resulting macrocyclic peptide contains two loops of amino acids, which is constrained with an azobenzene moiety that can change the conformation in response to visible light.

Recombinant botulinum neurotoxin serotype A1 in vivo characterization.

Clinically used botulinum neurotoxins (BoNTs) are natural products of Clostridium botulinum. A novel, recombinant BoNT type A1 (rBoNT/A1; IPN10260) has been synthesized using the native amino acid sequence expressed in Escherichia coli and has previously been characterized in vitro and ex vivo. Here, we aimed to characterize rBoNT/A1 in vivo and evaluate its effects on skeletal muscle. The properties of rBoNT/A1 following single, intramuscular administration were evaluated in the mouse and rat digit abduction score (DAS) assays and compared with those of natural BoNT/A1 (nBoNT/A1). rBoNT/A1‐injected tibialis anterior was assessed in the in situ muscle force test in rats. rBoNT/A1‐injected gastrocnemius lateralis (GL) muscle was assessed in the compound muscle action potential (CMAP) test in rats. The rBoNT/A1‐injected GL muscle was evaluated for muscle weight, volume, myofiber composition and immunohistochemical detection of cleaved SNAP25 (c‐SNAP25). Results showed that rBoNT/A1 and nBoNT/A1 were equipotent and had similar onset and duration of action in both mouse and rat DAS assays. rBoNT/A1 caused a dose‐dependent inhibition of muscle force and a rapid long‐lasting reduction in CMAP amplitude that lasted for at least 30 days. Dose‐dependent reductions in GL weight and volume and increases in myofiber atrophy were accompanied by immunohistochemical detection of c‐SNAP25. Overall, rBoNT/A1 and nBoNT/A1 exhibited similar properties following intramuscular administration. rBoNT/A1 inhibited motoneurons neurotransmitter release, which was robust, long‐lasting, and accompanied by cleavage of SNAP25. rBoNT/A1 is a useful tool molecule for comparison with current natural and future modified recombinant neurotoxins products.

JUMPt: Comprehensive Protein Turnover Modeling of In Vivo Pulse SILAC Data by Ordinary Differential Equations.

Recent advances in mass spectrometry (MS)-based proteomics allow the measurement of turnover rates of thousands of proteins using dynamic labeling methods, such as pulse stable isotope labeling by amino acids in cell culture (pSILAC). However, when applying the pSILAC strategy to multicellular animals (e.g., mice), the labeling process is significantly delayed by native amino acids recycled from protein degradation in vivo, raising a challenge of defining accurate protein turnover rates. Here, we report JUMPt, a software package using a novel ordinary differential equation (ODE)-based mathematical model to determine reliable rates of protein degradation. The uniqueness of JUMPt is to consider amino acid recycling and fit the kinetics of the labeling amino acid (e.g., Lys) and whole proteome simultaneously to derive half-lives of individual proteins. Multiple settings in the software are designed to enable simple to comprehensive data inputs for precise analysis of half-lives with flexibility. We examined the software by studying the turnover of thousands of proteins in the pSILAC brain and liver tissues. The results were largely consistent with the proteome turnover measurements from previous studies. The long-lived proteins are enriched in the integral membrane, myelin sheath, and mitochondrion in the brain. In summary, the ODE-based JUMPt software is an effective proteomics tool for analyzing large-scale protein turnover, and the software is publicly available on GitHub (https://github.com/JUMPSuite/JUMPt) to the research community.

Micelles Based on Lysine, Histidine, or Arginine: Designing Structures for Enhanced Drug Delivery.

Natural amino acids and their derivatives are excellent building blocks of polymers for various biomedical applications owing to the non-toxicity, biocompatibility, and ease of multifunctionalization. In the present review, we summarized the common approaches to designing and constructing functional polymeric micelles based on basic amino acids including lysine, histidine, and arginine and highlighted their applications as drug carriers for cancer therapy. Different polypeptide architectures including linear polypeptides and dendrimers were developed for efficient drug loading and delivery. Besides, polylysine- and polyhistidine-based micelles could enable pH-responsive drug release, and polyarginine can realize enhanced membrane penetration and gas therapy by generating metabolites of nitric oxide (NO). It is worth mentioning that according to the structural or functional characteristics of basic amino acids and their derivatives, key points for designing functional micelles with excellent drug delivery efficiency are importantly elaborated in order to pave the way for exploring micelles based on basic amino acids.

Molecular thermodynamics for amino‐acid adsorption at inorganic surfaces

AbstractThe interaction of polypeptides and proteins with an inorganic surface is intrinsically dependent on the interfacial behavior of amino acids and sensitive to solution conditions such as pH, ion type, and salt concentration. A faithful description of amino‐acid adsorption remains a theoretical challenge from a molecular perspective due to the strong coupling of local thermodynamic nonideality and inhomogeneous ionization of both the adsorbate and substrate. Building upon a recently developed coarse‐grained model for natural amino acids in bulk electrolyte solutions, here we report a molecular theory to predict amino‐acid adsorption on ionizable inorganic surfaces over a broad range of solution conditions. In addition to describing the coupled ionization of amino acids and the underlying surface, the thermodynamic model is able to account for both physical binding and surface associations such as hydrogen bonding or bidentate coordination. It is applicable to all types of natural amino acids regardless of the solution pH, salt type and concentration. The theoretical predictions have been validated by extensive comparison with experimental data for the adsorption of acidic, basic, and neutral amino acids at rutile (α‐TiO2) surfaces.

A novel method to produce synthetic murine CXCL10 for efficient screening of functional variants

Antitumor immune responses depend on the infiltration of solid tumors by effector T cells, a process guided by chemokines. In particular, the chemokine CXCL10 has been shown to play a critical role in mediating recruitment of CXCR3 + cytolytic T and NK cells in tumors, though its use as a therapeutic agent has not been widely explored. One of the limitations is due to the rapid inactivation of CXCL10 by dipeptidyl peptidase 4 (DPP4), a broadly expressed enzyme that is active in plasma and other bodily fluids. In the present study, we describe a novel method to produce synthetic CXCL10 that is resistant to DPP4 N-terminal truncation. Using a Fmoc solid-phase peptide synthesis approach, synthetic murine WT CXCL10 was produced, showing similar biochemical and biological properties to the recombinant protein. This synthesis method supported production of natural (amino acid substitution, insertion or deletion) and non-natural (chemical modifications) variants of CXCL10. In association with a functional screening cascade that assessed DPP4-mediated cleavage, CXCR3 signaling potency and chemotactic activity, we successfully generated 20 murine CXCL10 variants. Among those, two non-natural variants with N-methylated Leu3 (MeLeu3) and a reduced amide bond between Pro2 and Leu3 (rLeu3), respectively, showed resistance to DPP4 truncation but decreased CXCR3 signaling and chemotactic activity. Interestingly, MeLeu3 and rLeu3 CXCL10 behaved as DPP4 inhibitors, preventing the truncation of WT CXCL10. This study highlights the potential of using Fmoc solid-phase chemistry in association with biochemical and biological characterization to rapidly identify CXCL10 variants with desired properties. These novel methods unlock the opportunity to develop DPP4 resistant CXCL10 variants, as well as other chemokine substrates, while maintaining chemotactic properties.

Enantioselective Dynamic Exchange Reactions of Imines.

Although dynamic reactions of imines have been extensively studied, the dynamic behaviors manipulated by chirality remain nearly unexplored. In this work, enantioselective amine exchange reactions were demonstrated as a first example via the reaction of enantiomeric chiral amines such as natural amino acids with a series of innovative axially chiral 1,1'-binaphthyl-2,2'-diamine (BNDA)-based imines that were prepared from the condensation reactions between BNDA and salicylaldehyde (SA) or its derivatives. This enantioselective dynamic behavior can be directly indicated by the degree of the fluorescence response of the R-configuration of imines to the d-enantiomer of chiral amine, because the released BNDA can serve as the fluorescence signal output when the amine exchange reaction occurs, which is far higher than the response to its l-enantiomer under identical experimental conditions. For the S-configuration of chiral imines, the fluorescence response is the opposite. The enantioselective exchange reaction can be tuned by altering the electron-withdrawing or electron-donating capability of the substituent at position 4 or 5 of the SA part of chiral imines. Not only o-OH groups in SA-based imines but also protic solvents used as reaction media were found to be important to the dynamic behavior at high rates.

A Selection of Macrocyclic Peptides That Bind STING From an mRNA-Display Library With Split Degenerate Codons.

Recent improvements in mRNA display have enabled the selection of peptides that incorporate non‐natural amino acids, thus expanding the chemical diversity of macrocycles beyond what is accessible in nature. Such libraries have incorporated non‐natural amino acids at the expense of natural amino acids by reassigning their codons. Here we report an alternative approach to expanded amino‐acid diversity that preserves all 19 natural amino acids (no methionine) and adds 6 non‐natural amino acids, resulting in the highest sequence complexity reported to date. We have applied mRNA display to this 25‐letter library to select functional macrocycles that bind human STING, a protein involved in immunoregulation. The resulting STING‐binding peptides include a 9‐mer macrocycle with a dissociation constant (K D) of 3.4 nM, which blocks binding of cGAMP to STING and induces STING dimerization. This approach is generalizable to expanding the amino‐acid alphabet in a library beyond 25 building blocks.

A Selection of Macrocyclic Peptides That Bind STING From an mRNA‐Display Library With Split Degenerate Codons

AbstractRecent improvements in mRNA display have enabled the selection of peptides that incorporate non‐natural amino acids, thus expanding the chemical diversity of macrocycles beyond what is accessible in nature. Such libraries have incorporated non‐natural amino acids at the expense of natural amino acids by reassigning their codons. Here we report an alternative approach to expanded amino‐acid diversity that preserves all 19 natural amino acids (no methionine) and adds 6 non‐natural amino acids, resulting in the highest sequence complexity reported to date. We have applied mRNA display to this 25‐letter library to select functional macrocycles that bind human STING, a protein involved in immunoregulation. The resulting STING‐binding peptides include a 9‐mer macrocycle with a dissociation constant (KD) of 3.4 nM, which blocks binding of cGAMP to STING and induces STING dimerization. This approach is generalizable to expanding the amino‐acid alphabet in a library beyond 25 building blocks.

L-Serine, an Endogenous Amino Acid, Is a Potential Neuroprotective Agent for Neurological Disease and Injury.

Central nervous system (CNS) lesions are major causes of human death and disability worldwide, and they cause different extents of motor and sensory dysfunction in patients. Thus, it is crucial to develop new effective neuroprotective drugs and approaches targeted to the heterogeneous nature of CNS injury and disease. L-serine is an indispensable neurotrophic factor and a precursor for neurotransmitters. Although L-serine is a native amino acid supplement, its metabolic products have been shown to be essential not only for cell proliferation but also for neuronal development and specific functions in the brain. Growing evidence has suggested that L-serine regulates the release of several cytokines in the brain under some neuropathological conditions to recover cognitive function, improve cerebral blood flow, inhibit inflammation, promote remyelination and exert other neuroprotective effects on neurological injury. L-serine has also been used to treat epilepsy, schizophrenia, psychosis, and Alzheimer’s Disease as well as other neurological diseases. Furthermore, the dosing of animals with L-serine and human clinical trials investigating the therapeutic effects of L-serine generally support the safety of L-serine. The high significance of this review lies in its emphasis on the therapeutic potential of using L-serine as a general treatment for numerous CNS diseases and injuries. Because L-serine performs a broad spectrum of functions, it may be clinically used as an effective neuroprotective agent.

Acetonitrile adduct analysis of underivatised amino acids offers improved sensitivity for hydrophilic interaction liquid chromatography tandem mass-spectrometry

LC-MS/MS method development for native amino acid detection can be problematic due to low ionisation efficiencies, in source fragmentation, potential for cluster ion formation and incorrect application of chromatography techniques. This has led to the majority of the scientific community derivatising amino acids for more sensitive analysis. Derivatisation has several benefits including reduced signal-to-noise ratios, more efficient ionisation, and a change in polarity, allowing the use of reverse phase chromatography. However, derivatisation of amino acids can be expensive, requires additional sample preparation steps, is more time consuming and increases sample instability, due to the most derivatised amino acids only be stable for finite amount of time. While showing initial promise, development of reliable hydrophilic interaction liquid chromatography (HILIC) separation methods has presented difficulties for the analyst including irreproducible separation and poor sensitivity. This study aimed to find a means to improve the detection sensitivity of the 20 protein amino acids by HILIC-MS/MS. We describe the use of previously undescribed amino acid-acetonitrile (ACN) adducts to improve detection of 16 out of the 20 amino acids. While all amino acids examined did form an ACN adduct, 4 had low intensity adduct formation compared to their protonated state, 3 of which are classified as basic amino acids. For 15 of the 20 amino acids tested, we used the ACN adduct for both quantification and qualification ions and demonstrated a significant enhancement in signal-to-noise ratio, ranging from 23 to 1762% improvement. Lower LODs, LOQs and lower ranges of linearity were also achieved for these amino acids. The optimised method was applied to a human neuroblastoma cell line (SH-SY5Y) with the potential to be applied to other complex sample types. The improved sensitivity this method offers simplifies sample preparation and reduces the costs of amino acid analysis compared to those methods that rely on derivatisation for sensitivity.

CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations.

Preparing molecular coordinate files for molecular dynamics (MD) simulations can be a very time-consuming process. Herein we present the development of a user-friendly program that drastically reduces the time required to prepare these molecular coordinate files for MD software packages such as AmberTools. Our program, known as charge atomtype naming (CAN), creates and uses a library of structures such as amino acid monomers to update the charge, atom type, and name of atoms in any molecular structure (mol2) file. We demonstrate the utility of this new program by rapidly preparing structural files for MD simulations for polypeptides ranging from small molecules to large protein structures. Both native and non-native amino acid residues are easily handled by this new program.

Peptide Stapling Improves the Sustainability of a Peptide-Based Chimeric Molecule That Induces Targeted Protein Degradation.

Peptide-based target protein degradation inducers called PROTACs/SNIPERs have low cell penetrability and poor intracellular stability as drawbacks. These shortcomings can be overcome by easily modifying these peptides by conjugation with cell penetrating peptides and side-chain stapling. In this study, we succeeded in developing the stapled peptide stPERML-R7, which is based on the estrogen receptor alpha (ERα)-binding peptide PERML and composed of natural amino acids. stPERML-R7, which includes a hepta-arginine motif and a hydrocarbon stapling moiety, showed increased α-helicity and similar binding affinity toward ERα when compared with those of the parent peptide PERML. Furthermore, we used stPERML-R7 to develop a peptide-based degrader LCL-stPERML-R7 targeting ERα by conjugating stPERML-R7 with a small molecule LCL161 (LCL) that recruits the E3 ligase IAPs to induce proteasomal degradation via ubiquitylation. The chimeric peptide LCL-stPERML-R7 induced sustained degradation of ERα and potently inhibited ERα-mediated transcription more effectively than the unstapled chimera LCL-PERML-R7. These results suggest that a stapled structure is effective in maintaining the intracellular activity of peptide-based degraders.

APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures.

Good knowledge of a peptide’s tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational protocol that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5–40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9Å from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and PepLook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.

Recent Applications of Retro-Inverso Peptides.

Natural and de novo designed peptides are gaining an ever-growing interest as drugs against several diseases. Their use is however limited by the intrinsic low bioavailability and poor stability. To overcome these issues retro-inverso analogues have been investigated for decades as more stable surrogates of peptides composed of natural amino acids. Retro-inverso peptides possess reversed sequences and chirality compared to the parent molecules maintaining at the same time an identical array of side chains and in some cases similar structure. The inverted chirality renders them less prone to degradation by endogenous proteases conferring enhanced half-lives and an increased potential as new drugs. However, given their general incapability to adopt the 3D structure of the parent peptides their application should be careful evaluated and investigated case by case. Here, we review the application of retro-inverso peptides in anticancer therapies, in immunology, in neurodegenerative diseases, and as antimicrobials, analyzing pros and cons of this interesting subclass of molecules.

Is the Volume Exclusion Model Practicable for Nanopore Protein Sequencing?

The nanopore approach holds the possibility for achieving single-molecule protein sequencing. However, ongoing challenges still remain in the biological nanopore technology, which aims to identify 20 natural amino acids by reading the ionic current difference with the traditional current-sensing model. In this paper, taking aerolysin nanopores as an example, we calculate and compare the current blockage of each of 20 natural amino acids, which are all far from producing a detectable current blockage difference. Then, we propose a modified solution conductivity of σ' in the traditional volume exclusion model for nanopore sensing of a peptide. The σ' value describes the comprehensive result of ion mobility inside a nanopore, which is related to but not limited to nanopore-peptide interactions, and the positions, orientations, and conformations of peptides inside the nanopore. The nanopore experiments of a short peptide (VQIVYK) in wild type and mutant nanopores further demonstrate that the traditional volume exclusion model is not enough to fully explain the current blockage contribution and that many other factors such as enhanced nanopore-peptide interactions could contribute to a dominant part of the current change. This modified sensing model provides insights into the further development of nanopore protein sequencing methods.

Development of electronic modules for their integration with impedimetric transducers applied to sarcosine detection

The development of fast, simple, sensitive, and minimally invasive biosensors for detecting diseases, conventionally need specialized, expensive, and highly invasive instrumentation. Furthermore, such biosensors pertinently also, need the development of optoelectronic modules that are capable of implementing specific detection techniques while interacting with the user through a friendly interface. This work highlights the development of a system whose hardware and software contributes to the detection of analytes by impedimetric sensors, especially emphasizing on the detection of sarcosine, a natural amino acid associated with prostate cancer (PCa). Dummy circuits coupled with impedimetric transducers were used to perform precise measurements using a sinusoidal signal of 20 mV in the range from 0.1 Hz to 1 MHz.