Lysine Amino Acids: Properties, Function, Benefits, and Sources

What is lysine?

Lysine cannot be produced by the majority of higher organisms and is hence an essential amino acid (IAA) that must be ingested in sufficient quantities to support protein synthesis. Despite lysine being a prevalent amino acid in bodily proteins, its availability is restricted in numerous significant food sources (e.g., cereals). Previous results emphasized the significance of lysine, since animals on a lysine-deficient diet exhibited slower weight loss compared to those on other IAA-deficient diets, suggesting the existence of a unique reservoir of lysine or its metabolites that might be converted into lysine. The initial stage of the lysine catabolic route involves the synthesis of saccharopine, followed by the production of 2-aminoadipic acid, both of which occur in the mitochondria. The metabolism of 2-aminoadipic acid occurs through decarboxylation, resulting in a sequence of CoA esters culminating in acetyl-CoA. In animals, the liver serves as the principal location for lysine catabolism. The metabolic and oxidative response of lysine in humans to diets either deficient in protein or lysine aligns with measurements obtained for other essential amino acids using isotopically tagged tracers. Intestinal bacteria convert urea into ammonia and extract nitrogen (N) for amino acid synthesis. Research involving the administration of ¹⁵N-ammonium chloride or ¹⁵N-urea to both animals and people reveals the emergence of ¹⁵N-lysine in microbial lysine within the intestine as well as in the lysine of the host.

Lysine structure and Lysine charge

Similar to other amino acids, lysine possesses an amino group and a carboxyl group. However, Lysine possesses a side chain characterized by an elongated aliphatic chain ending with an ε-amino group (–NH₂), rendering it basic and positively charged in physiological settings. The positively charged ε-amino group renders lysine a polar and hydrophilic amino acid.

Molecular structure of L-arginine, L-lysine and L-alanine. (Parikh K D., et al., 2016)

Lysine pKa

The side chain of the lysine amino acid has one main ɛ-amino group that has a pKa of 10.05. Reactive carbonyl compounds have easy access to this positively charged residue, which is solvent exposed on protein surfaces.

L-Lysine and L-arginine: pharmacological information. (Pedrazini M C., et al., 2022)

Lysine modifications

Over the past decade, numerous novel acyl-lysine modifications have been documented on proteins, including butyrylation, crotonylation, succinylation, malonylation, glutarylation, hydroxyisobutyrylation, 2-hydroxybutyrylation, and long-chain fatty acylation. The physiological importance of these novel acyl-lysine alterations is only starting to be clarified.

Structures of lysine modifications. (Wang M., et al., 2021)

Lysine amino acids at Creative Peptides

Lysine acetylation

The initial description of lysine acetylation in histones was provided by Vincent Allfrey and his associates in 1964. Lysine acetylation is a conserved and reversible posttranslational modification (PTM) in eukaryotes that regulates protein activities by transferring an acetyl group from acetyl coenzyme A (Ac-CoA) to the ε-amino side chain of a lysine residue in proteins. Lysine acetylation transpires in both histones and non-histone proteins. Lysine acetylation of histones, including Histone 2A (H2A), Histone 2B (H2B), Histone 3 (H3), and Histone 4 (H4), typically leads to transcriptional activation by destabilizing DNA-histone interactions. This occurs because lysine acetylation neutralizes its positive charge, thereby inhibiting the formation of salt bridges with the negatively charged phosphate backbone of DNA. Alongside histones, numerous nonhistone proteins within the cytoplasm and organelles undergo dynamic acetylation and deacetylation; these modifications are intricately involved in the regulation of diverse cellular processes, such as gene transcription, cell cycle progression, DNA damage repair, cellular signal transduction, protein folding stability and aggregation, cytoskeleton organization, RNA processing and stability, and autophagy regulation.

The acetylation of lysine residues can be facilitated by KATs or altered by the plentiful Ac-CoA via nonenzymatic processes. Lysine deacetylation, on the other hand, is facilitated by KDACs, which consist of two primary categories with differing catalytic mechanisms: NAD+-dependent Sirtuins (SIRTs) and Zn²⁺-dependent histone deacetylases (HDACs). Lysine acetylation levels are highly dynamic, with the equilibrium between acetylation and deacetylation meticulously regulated by KATs and KDACs, with the concentration of Ac-CoA in organellar compartments like mitochondria.

The "histone code" consists of several PTMs, including acetylation, phosphorylation, methylation, ubiquitination, and others. One theory proposes that these modifications, either alone or in combination, influence the structure and functions of chromatin. Histones are a large class of substrates for lysine acetylation. A number of critical cellular processes and disease progression are impacted by histone acetylation and other post-translational modifications (PTMs), which can either attract or reject chromatin regulatory protein complexes. These complexes control gene expression and other genomic functions. In general, when histones are acetylated by KATs, they loosen their binding to DNA, which in turn turns on gene transcription. On the other hand, when histones are deacetylated by HDACs, chromatin condenses and gene transcription is turned off. Histone acetylation also increases the number of regulatory factors by allowing it to interact with transcriptional factors and proteins that possess bromodomains. Histones are more likely to bind to transcriptional co-repressors when they are hypoacetylated; moreover, certain KDACs can either impede transcription initiation or be recruited to prepare for transcription repression.

When comparing dopaminergic (DA) neurons from midbrain tissues of Parkinson's disease (PD) patients with matched controls, Park's team discovered significantly greater levels of lysine acetylation at various histone locations, including H2A, H2B, H3, and H4. Downregulation of key histone deacetylases (KDACs) including HDAC1, HDAC2, HDAC4, HDAC6, and SIRT1 likely causes histone acetylation to be upregulated, whereas CBP, TIP60, and GCN5 remain relatively unaffected. H3K14 and H3K18 acetylation are the principal targets of elevated H3 acetylation in the primary motor cortex of postmortem Parkinson's disease, according to another study. Furthermore, the progression of PD is disease-dependently linked to elevations in histone acetylation.

Overview of lysine acetylation and deacetylation. (Wang R., et al., 2020)

Lysine methylation

The discovery of protein methylation's function in gene expression via histone modification in 1964 initially attracted substantial research interest. Proteins can be methylated by a variety of enzymes called methyltransferases (MTases), which transform the universal methyl donor S-adenosylmethionine (SAM) into S-adenosylhomocysteine (SAH) by transferring a methyl group from SAM to different substrates. Mono-, di-, or trimethyl groups (Kme1, Kme2, or Kme3, respectively) are chemically attached to the ε-nitrogen of specific lysine residues on target proteins in the process of protein lysine methylation. The enzymes lysine methyltransferases (KMTs) and lysine demethylases (KDMs) regulate the dynamic process of lysine methylation in proteins. KMTs add methyl groups to lysine residues, while KDMs remove them. "Writers" is a more accurate term for KMTs, whereas "erasers" is a more accurate description of KDMs.

In reaction to several regulatory cues, glucose metabolism, a key cellular activity, maintains an energy balance. The absorption of glucose is an important factor in cellular glucose metabolism because it helps keep glucose levels stable by balancing the generation of glucose by the liver with their uptake. The efficiency of glucose uptake in carbohydrate metabolism may be influenced by lysine methylation, according to multiple studies. As an example, there is evidence that the methyltransferase SMYD2 controls glucose absorption. By enhancing the protein stability of c-Myc through methylation, SMYD2 inhibition changes glucose absorption. One way that SETD1A, an H3K4 lysine methyltransferase, decreases glucose absorption is by lowering the expression of genes including HK2, PFK2, and PKM2. Set7, a lysine methyltransferase that contains the SET domain, inhibits the expression of HIF-1α/2α targets by methylating HIF-1α at lysine 32 and HIF-2α at lysine 29. Hypoxic circumstances enhance glucose uptake when Set7 is inhibited or knocked down, suggesting that Set7-mediated lysine methylation controls HIF-1α transcriptional activity and HIF-1α-mediated glucose homeostasis in a negative way. Inhibiting lysine-specific demethylase-1 (LSD1, KDM1A), which is crucial for metabolic homeostasis, reduces glucose absorption and leads to metabolic disruption. To activate the glycolytic pathway and mitochondrial respiration in esophageal cancer cells, knocking down LSD1 dramatically decreases invasive activity and glucose uptake, decreases their extracellular acidification rate (ECAR), and increases their oxygen consumption rate (OCR) and OCR/ECAR ratio.

Diagram of the methyltransferase catalytic reaction. (Wang Z., et al., 2024)

Lysine crotonylation

A post-translational alteration called lysine crotonylation has just been found. It differs structurally and functionally from lysine acetylation, which has been the subject of much research. Lysine crotonylation regulates chromatin remodelling, metabolism, the cell cycle, and cellular organization, among other biological processes. New mass spectrometry-based methods for identifying and quantifying lysine crotonylation have shown that non-histone proteins are often crotonylated. The enzyme balance between lysine crotonylases and crotonyltransferases is always changing. Catalyzing the covalent alteration of lysine crotonylation, the crotonyltransferases were once known as writers. Additionally, histone crotonyltransferase (HCT) activities were demonstrated in the histone acetyltransferases (HATs). The three main families of histone acetyltransferases (HATs) are the p300/CBP, GNAT, and MYST families, which are defined by different sequences and structural properties. The GNAT family is ubiquitous and conserved throughout all kingdoms of life, in contrast to the eukaryotic-specific p300/CBP and MYST families.

Histone crotonylation is an important regulator of gene transcription, as was initially shown by Tan's group. In the genomes of human somatic cells and male germ cells from mice, histone crotonylation was discovered to identify enhancers and the transcription start site of active genes. Also, in the male germinal cells just after meiosis, histone crotonylation was more prevalent on sex chromosomes and identified X-linked genes that had managed to evade sex chromosomal inactivation. More so than histone acetylation, p300-mediated histone crotonylation promotes gene transcription, according to a new study. Their cell-based model of transcriptional activation also indicated that changes in gene expression were associated with variations in the quantity of crotonyl-CoA in cells, which in turn caused variations in the levels of histone crotonylation surrounding activated gene regulatory elements. Utilizing the innovative CBP/p300 mutants (p300 I1395G and CBP I1432G) that had impaired histone acetyltransferase but competent histone chromatin remodelling (HCT) activity, Liu's group established that CBP/p300 can enhance transcriptional activation when HAT is absent but HCT activity is present. Using new HDAC1 and HDAC3 mutants (HDAC1/3-VRPP) with defective HDAC but intact HDCR activity, their research mates later discovered that selective HDCR in mammalian cells coincides with a broad transcriptional suppression.

Protein crotonylation. (Wan J., et al., 2019)

Functional roles of lysine crotonylation. (Wan J., et al., 2019)

Lysine ubiquitination and sumoylation

Ubiquitination and sumoylation can be polymeric in nature, in contrast to lysine acetylation and methylation, which are tiny molecule changes. Ubiquitination refers to the process by which proteins are covalently linked to the 76-amino acid polypeptide ubiquitin. An isopeptide bond is usually formed between the carboxylic acid group of the final amino acid (G76) of the tiny protein ubiquitin and the epsilon amino group of a lysine residue on the target protein. This is the outcome of a three-tiered enzymatic cascade. The process of ubiquitination might involve the addition of a single ubiquitin to a specific lysine (monoubiquitination), multiple ubiquitin molecules (polyubiquitination), or structures including differently linked ubiquitin chains (diubiquitination). In a similar vein, sumoylation covalently conjugates SUMO proteins—which typically consist of about 100 amino acids—to proteins. The initial discovery of the processive destruction of ubiquitinated proteins was made by an ATP-dependent protease, which was subsequently referred to be the 26S proteasome. Recent years have shown that ubiquitination is involved in more than just proteosomal degradation; it regulates a wide range of cellular processes, including protein activation and/or inactivation, localization of proteins, and interactions between proteins. These processes have functional implications for cell viability, cell cycle, protein synthesis, DNA repair, transcriptional regulation, protein trafficking, and stress responses.

What does lysine do?

Lysine is an essential amino acid because mammals cannot produce it on their own. Because it, like threonine, does not take part in transamination events, lysine is an absolutely necessary amino acid. Lysine basically just helps out with protein synthesis. The irreversible production of glutamate and α-aminoadipate, which are subsequently subjected to deamination and oxidation, is another outcome of the saccharopine pathway catabolism of lysine in mammals. It is mostly in the liver that lysine is catabolic. Enterocytes may be able to oxidize lysine in response to high protein consumption, according to some studies in piglets but not in babies. However, there is no proof that enterocytes express the enzymes required for lysine catabolism. Aside from its significance in protein synthesis, lysine is needed for the production of carnitine, an essential component in β-oxidation.

Although the chemical reactivity of lysine and arginine side chains is comparable, lysine residues are significantly more susceptible to post-translational modifications (PTMs). The capacity of the arginine guanidinium group to establish three-dimensional ionic connections enables arginine to assume a significant structural role, facilitating protein folding and stability. Lysine's polarity contributes to protein structure, while its amine group can establish a single ionic connection, rendering lysine functionally more versatile and susceptible to modification. The relative flexibility in ionic coordination and the chemical reactivity of the main amine group render lysine a significant participant in numerous enzyme catalysis pathways. Examples include ATP-dependent protein kinases, whereby a lysine located in the catalytic site participates in the phosphotransfer reaction. This trait has been utilized by microbes to circumvent host defenses: wortmannin inactivates PI3K-like proteins through covalent binding to lysine residues in the catalytic site. Lysine may also engage indirectly in enzyme catalysis by covalently binding cofactors such as biotin (vitamin B7), which is crucial for catalysis in carboxylation processes. Consequently, a primary impetus for the first diversification of lysine post-translational modifications may have been the necessity to mitigate the reactive 'catalytic' characteristics of this amino acid. This may have facilitated the formation of an enzyme catalytic pocket containing active lysine residues, while surface-localized residues would be obstructed by post-translational modifications. Numerous lysine post-translational modifications are directly influenced by the availability of particular metabolic substrates (e.g., acetyl-CoA, SAM, ATP) and, consequently, variably perceive the cellular metabolic state. Thus, the fundamental characteristics of lysine render these post-translational modifications extremely significant for the regulation of cellular health.

Requirements and functions of lysine and tryptophan in the human body. (Hossain F., et al., 2019)

What is Lysine used for?

(1) Produce nanoparticles

The positive side chains of lysine are fully protonated at physiological pH (pKa ∼10.5), which allows it to bind anion efficiently, which contributes to its well-documented efficacy in polyplex production. Because of the electrostatic binding to proteoglycans on cell surfaces, polyplexes become more stable outside of cells and are more easily taken up by cells through endocytosis. The most popular polypeptidic gene delivery vector, poly-l-lysine (PLL), is a homopolymer that is typically made from lysine. Gene delivery in vitro and in vivo can be mediated via PLL, a biodegradable polymer. PLL is offered by vendors in a range of molecular weights, from about 1 to 300 kDa. When compared to other polypeptidic vectors, its pKa value of approximately 10 is quite high. Enzymatic and hydrolytic breakdown of nucleic acids can be prevented by using this feature to bundle them into nanoparticulate complexes, which disguise the negative charge of DNA and RNA. Compared to low-molecular-weight PLL, high-molecular-weight PLL forms tighter, smaller, and more stable complexes due to its increased net positive charge. However, it has been found to exhibit high levels of cytotoxicity. When compared to poly(ethyleneimine) (PEI), PLL is often thought of as being less effective in facilitating endosomal escape and transfection efficiency. A combination of endosomolytic reagents, such as chloroquine or a fusogenic peptide, was required to improve gene expression in vitro when PLL was used alone. PLL has been directly modified to make it a better vector, with cleavable bonds added to its backbone or side chains, which decreases in vivo toxicity and increases transfection efficiency by facilitating the release of nucleic acid. Sugars, folic acid derivatives, antibodies, and targeting ligands (e.g., Tf) can be attached to receptors to enable receptor-mediated gene delivery. Combination with other peptides, such as cell-penetrating peptides (CPPs) or fusogenic peptides, or modification with histidine to aid endosomal escape, has also been found to increase the transfection efficacy of PLL.

(2) Reduce ulcer occurrence

Among the eight amino acids that are absolutely required for human metabolism, lysine plays a pivotal function. For the treatment and prevention of herpes labialis, the most frequent recurrent illness caused by the herpes simplex virus, lysine is commonly utilized, both topically and as a herbal supplement. The basic idea behind lysine treatment is that it decreases the amount of cellular arginine available, which in turn suppresses the herpes simplex virus reproduction process. Commercially available lysine, in its biologically active form known as L-lysine, is often sold as 500 mg tablets as a monohydrochloride salt. Topical use of monohydrochloride crystalline lysine can be used to treat herpes simplex virus infections. Although lysine has been demonstrated to decrease ulcer occurrence, size, duration, and quantity, the efficacy of the therapies has been inconsistent among studies that have utilized varying dosages (500 mg/day to 1500 mg/day). To closely control for dietary sources of arginine and lysine, more research should be encouraged to discover appropriate amounts for efficacy.

(3) Promote absorption of calcium

Excess lysine in healthy individuals is metabolized, meaning excess amino acids are broken down into their respective carbon chains and amino group. These metabolites are then excreted, however in rare metabolic changes with lysinuria and cystinuria, which must be controlled because of the risk of death, particularly in neonates, lysine in its free form can be excreted. After attaching to a cell, lysine begins to carry out its activities, which include the conversion of glucose to acetyl CoA, an amino acid precursor to L-carnitine, and its role in carbohydrate metabolism, which helps generate energy. Due to its use of fatty acids for energy synthesis in mitochondria, L-carnitine is thought to have a ketogenic effect. L-lysine is prescribed to treat osteoporosis because it aids in the production of collagen and elastin and promotes the intestinal absorption of calcium.

(4) Neural activity regulation

Lysine regulates neuronal proliferation, differentiation, and excitability, and is thought to be the amino acid found in the greatest concentration in neuronal proteins. By enhancing the affinity of the GABA-benzodiazepine receptor complex, it influences neurotransmitter activity and produces anxiolytic effects. Lysine can raise the pain threshold, according to animal research.

(5) Antiviral activity

Indirectly protecting against Alzheimer's disease, Lysine's antiviral properties in treating herpes simplex reduce the likelihood of neurological damage. Because lysine inhibits both viral recurrence and neurodegenerative illness, it is doubly protective due to the association between HHV-1 and Alzheimer's. Accelerated tissue regeneration and infection control are promoted by its involvement in collagen formation and antibody production. Research has demonstrated that this amino acid improves the healing process of herpesvirus (HHV) lesions, decreases the number of lesions (HHV-6/7), and lessens the severity of lesions (HHV-1 and HHV-6/7). There was an activity in controlling the clinical evolution of lesions, typically suppressing the development of initial lesions (HHV-1), and a rise in the interval between outbreaks, with a reduction in recurrence episodes per year.

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