How Vitamins Work

(Note: the following is for educational purposes only. Most of the figures are taken from Lehninger’s ‘Principles of Biochemistry (5th edition) textbook, other figures are taken from different internet sources or from academic articles. For these, I provide a link where possible)

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I. OVERVIEW

What are vitamins?

Vitamins are organic molecules required in small quantities for the proper function of our body. Since we are unable to synthesize vitamins, completely or in sufficient amounts, we must obtain them from the diet. Vitamins can be divided to groups by different criteria. A long-used criterion is their water/fat solubility; most vitamins are water-soluble while some (vitamins K,A,D,E) are fat-soluble. This has implications for their absorption from the diet, as well as for their storage and clearance from the body.

Another criterion that is used for grouping vitamins is their general metabolic role; most vitamins belong to the ‘B-complex’ group, which is involved in central metabolic processes such as energy production from carbohydrates, fats and proteins, as well as their biosynthesis (see Table 1 below). This group includes vitamins B1 (thiamine), B2 (riboflavin), B3 (niacin), B5 (pantothenic acid), B6 (pyridoxine), B7 (biotin), B9 (folic acid) and B12 (cobalamin). As described in detail in section III below, the involvement of B-complex vitamins in central metabolism results from their ability to serve as enzyme co-factors (i.e. co-enzymes) in key biochemical pathways.

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Non-B-complex vitamins are involved in more specific cellular & physiological processes. Here is a short description of their involvement:

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Vitamin A (retinol) is essential for eye sight; its active form (retinal) is part of rhodopsin – the protein with which our eyes convert light to neural impulses that are ultimately translated to images in the brain. Deficiency in vitamin A leads to impaired vision, especially night blindness. In addition, vitamin A has been implicated in wound healing and in other physiological processes. In these cases, however, it acts in a completely different way as it does in vision.

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Vitamin C (ascorbic  acid) acts in the strengthening of collagen structure, the principle protein of connective tissues (skin, cartilage, bone, etc.). Vitamin C deficiency leads to unstable connective tissues, which results in scurvy, a disease well-known to 15th Century sailors. In scurvy, the loss of structural integrity of connective tissues manifests, among other things, in loose teeth and bleeding gums, skin lesions, and blood blisters on the skin. Like vitamin A and E (see below), vitamin C has also been implicated in wound healing.

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Vitamin D (calciferol) functions primarily in keeping our bones strong; its active form, calcitriol, function as a hormone that promotes the fortification of bones by calcium. It does that by inducing the genetic expression of different proteins involved in calcium absorption and use in our body. For example, it induces the expression of different calcium transport proteins in the intestines. This allows our body to get all the calcium it needs from food in order to build our bones. It therefore not surprising that vitamin D deficiency increases the risk of osteoporosis, a disease characterized by decreased bone mass and increase chances of fractures. There is evidence that vitamin D is also involved in activation of our immune system and the synthesis of various biologically important molecules, e.g. neurotrophic factors. Interestingly, vitamin D can also be synthesized in our body; when UV sunlight hits cholesterol molecules in our skin, it promotes a cascade of chemical reactions that turn these molecules into vitamin D derivatives. However, even in countries with ample sunlight this form of vitamin D synthesis is insufficient, and it also had to be obtained from the food.

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Vitamin E (tocopherol) is mainly known as an antioxidant; as such, it contributes to alleviating oxidative stress which results from both endogenic processes and exogenic factors (drugs, environmental pollutants). However, vitamin E also function as a biological regulator of different processes. It has been implicated in wound healing, growth of smooth muscles, and even blood clotting.

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Vitamin K (menaquinone) is essential for proper blood clotting. At the molecular level, this is achieved by using vitamin E as an enzyme co-factor in the synthesis of certain clotting factors (II (Prothrombin), VII, IX, X). Deficiency in vitamin K leads bleeding disorders, with symptoms like anemia, bruising, bleeding of the gums or nose, and heavy menstrual bleeding in women.

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What are the dietary sources of vitamins?

 Table 0

(click to enlarge)

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How do vitamins actually work?

Many people are familiar with the different types of vitamins and their occurrence in different food types, but not with how they exercise their important effects. As mentioned above, vitamins are chemically modified in our body into an active form. In most vitamins, this active form serves as a protein co-factor. That is, a molecule that binds to a protein (usually enzyme), and executes a specific molecular function that allow the protein to fulfill its biochemical role. Why do proteins need these co-factors at all? – Proteins are essentially made of amino acids. These organic molecules are chemically diverse and allow proteins to carry out many different molecular functions (in the molecular world chemical diversity = function diversity). However, some functions are chemically difficult to execute, in which case proteins use co-factors (when the protein is an enzyme is the co-factor is called ‘co-enzyme’). When the protein is an enzyme, the vitamin-derived co-factor is called ‘co-enzyme‘. All B-complex vitamins are used as co-enzymes, facilitating enzyme-mediated reactions that are chemically complex or just difficult.

A common example for such a reaction is the breaking stable C-C bonds. Some enzymes called ‘decarboxylases’ need to break a C-C bond to release a carboxyl group from the molecule on which they act. To do this they use the vitamin B1-derived co-enzyme thiamine diphosphate (TDP, Figure 1). TDP contains a positively charged aromatic ring that binds to the enzyme’s substrate in the active site and draws electrons from the C-C bond adjacent to the carboxyl group.  This significantly weakens the bond to the point of breaking, thus achieving the release of the carboxyl group (see more details in the next section below).

 Figure 1

Figure 1. Formation of TPP from vitamin B1 (thiamine)
(source: http://www.mikeblaber.org/oldwine/BCH4053/Lecture33/Lecture33.htm)

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II. SUMMARY: VITAMINS & CO-FACTORS

Table 1 below summarizes the biochemical and physiological functions of vitamin-derived co-factors. A more elaborate explanation of B-complex vitamin-derived co-enzymes is given in section III.

Table 1aTable 1bTable 1c

Table 1. Summary of vitamin-derived co-factors

(note the 3 separate table. Click each to enlarge)

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III. MOLECULAR MECHANISMS OF B-VITAMINS-DERIVED CO-FACTORS

Thiamine Diphosphate (TDP, TPP)

Source: vitamin B1 (thiamine, see Figure 1 above).

Biochemical reactions: aldehyde transfer, cleavage of bonds involving carbonyl groups (decarboxylation, transketolation).

Physiological importance: generation of energy from carbohydrates, RNA/DNA production, nerve function (synthesis of the neurotransmitter acetylcholine and of the myelin sheath covering nerve axons).

Deficiency-associated disease: beriberi, Wernicke-Korsakoff syndrome, demyelination of nerve cells.

Enzymes (examples):

  • Pyruvate dehydrogenase (Figure 2)
  • alpha-ketoglutarate dehydrogenase [Krebs cycle]
  • Transketolase [pentose-phosphate cycle]

 

Mechanism:

Oxidative decarboxylation is the loss of a CO2 from a carboxylic acid and a concomitant oxidation of the remained molecule (for example, the conversion of pyruvate to acetyl-CoA (Figure 2) – an important part of energy production from carbohydates).

 Figure 2

Figure 2. The oxidative decarboxylation of pyruvate to acetyl-CoA

The decarboxylation step of this complex process requires:

  1. A good nucleophile that would attack the carboxyl carbon.
  2. An electron acceptor to dissipate the negative charge that builds up on the α-carbon once the tetrahedral intermediate is formed.

While some protein amino acids may fulfill the first requirement, none can fulfill both. TPP has a thiazolium ring, which can do that thanks to the ability of its N+ atom to act as an electron sink. This manifests in the two first steps of the process:

1. The N+ atom of TPP draws electrons from one of the carbon atoms of TPP until it deprotonates to form a highly nucleophilic carbanion (Figure 2).

Figure 3

Figure 3. Deprotonation of TPP to a carbanion

The carbanion then attacks the substrate’s C2 atom (Figure 4, step 1).

2. The N+ atom of TPP’s thiazolium ring now draws electrons from the substrate’s Ca-C bond, resulting in its cleavage and decarboxylation (Figure 4. step 2).

Figure 4

Figure 4. The TPP-facilitated decarboxylation of pyruvate

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Flavin co-factors: FAD/FMN

Source: vitamin B2 (riboflavin)

Variations: FAD and FMN are related co-factors; they have the same isoalloxazine ring, which is also the active part (Figure 5). However, FAD is a dinucleotide whereas FMN is a mononucleotide – it lacks the second phosphate and the adenosyl moiety of FAD. This allows the two flavin co-factors to bind different proteins and therefore participate in different processes. Both FAD and FMN are prosthetic groups – they are tightly bound to the protein at all times.

Physiological importance: energy production from foodstuff, fatty acid breakdown, lipid synthesis.

Deficiency-associated disease: ariboflavinosis

Enzymes (examples):

FAD:

  • Pyruvate dehydrogenase [carbohydrate breakdown] (Figure 2)
  • Succinate dehydrogenase [Krebs cycle]
  • Glycerol 3-phosphate dehydrogenase [triglyceride/phospholipid synthesis]
  • Acyl-CoA dehydrogenase [fatty acid breakdown]
  • Glutathione reductase [antioxidation]

FMN:

NADH dehydrogenase [mitochondrial electron transfer chain]

 

Biochemical reactions & mechanism: FAD and FMN transfer electrons in various oxidation-reduction (‘redox’) reactions in the cell. Their isoalloxazine ring is able to receive two reducing equivalents (2H:) and to pass them on to an acceptor.

Figure 5

Figure 5. The molecular structure of FAD/FMN and the oxidation/reduction of their isoalloxazine ring.

Thanks to their ability to receive/give one or two electrons, they participate in a variety of redox reaction, catalyzed by dehydrogenases, oxidases, oxygenases, and other enzymes. The direct redox partners of flavoproteins can include two-electron acceptors such as NAD+ and NADP+ (see below) or one-electron acceptors such as the ferric hemes, iron–sulfur clusters and quinones.

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Nicotinamide co-factors: NAD+ & NADP+

Source: vitamin B3 (niacin)

Deficiency-associated disease: pellagra (causing the 3 D’s: Dermatitis, Diarrhea, Dementia)

Variations: NAD+ and NADP+ have the same dinucleotide structure, with the nicotinamide group being the active part of the molecule (Figure 6). NADP+ has an additional phosphate group at the non-active part of the molecule, which allows it to bind other enzymes than NAD+.

Enzymes (examples):

NAD+

  • Glyceraldehyde 3-phosphate dehydrogenase [glycolysis/gluconeogenesis]
  • Lactate dehydrogenase [lactate fermentation]
  • Alcohol dehydrogenase [ethanol fermentation]
  • Pyruvate dehydrogenase
  • Isocitrate dehydrogenase [Krebs cycle]
  • alpha-ketoglutarate dehydrogenase [Krebs cycle]
  • Malate dehydrogenase [Krebs cycle]
  • NADH dehydrogenase [oxidative phosphorylation]
  • beta-hydroxyacyl-CoA dehydrogenase [fatty acid breakdown]
  • Glutamate dehydrogenase [oxidative deamination – amino acid breakdown]
  • Glycerol 3-phosphate dehydrogenase [triglyceride/phospholipid synthesis]
  • beta-hydroxybutyrate dehydrogenase [ketone bodies synthesis/breakdown]

NADP+

  • Isocitrate dehydrogenase [Krebs cycel]
  • Glutamate dehydrogenase [amino acid breakdown]
  • Glucose 6-phosphate dehydrogenase (G6PD) [pentose-phosphate pathway]
  • 6 phosphogluconate dehydrogenase [pentose-phosphate pathway]
  • Glutathione reductase [antioxidation]
  • Malic enzyme [fatty acid synthesis (ACoA transport to cytosol)]
  • Fatty acid synthase [fatty acid synthesis]
  • Fatty acyl-CoA desaturase [double bond introduction to fatty acids]
  • HMG-CoA reductase [cholesterol synthesis]
  • Squalene synthase [cholesterol synthesis]
  • Squalene monooxygenase [cholesterol synthesis]

 

Biochemical reactions & mechanism: like FAD and FMN, NAD+ and NADP+ reversibly transfer reducing equivalents in the cell (Figure 6). However, there are two differences between the flavin and nicotinamide co-factors:

  1. The reducing equivalent in the case of NAD+ and NADP+ is a hydride ion (H), and not 2H: as in FAD/FMN.
  2. The nicotinamide ring of NAD+ and NADP+ is able to receive/give only two electrons at a time. Therefore, NAD+ and NADP+ participate in a smaller variety of reactions than FAD/FMN.

Figure 6

Figure 6. The molecular structure of NAD+/NADP+ and the oxidation/reduction of their nicotinamide.

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Coenzyme A (CoA)

Source: vitamin B5

Biochemical reactions: acyl transfer and carboxylate activation.

Physiological importance: energy production from foodstuff, synthesis of amino acids, lipids & neurotransmitters (acetylcholine).

Deficiency-associated condition: paresthesia

Enzymes (examples):

  • Pyruvate dehydrogenase (PDH)
  • a-keto glutarate dehydrogenase [Krebs cycle]
  • Acyl-CoA synthase [fatty acid breakdown]
  • Carnitine acyl transferase II [fatty acid breakdown]
  • Thiolase [fatty acid b-oxidation]
  • Fatty acid synthase [fatty acid synthesis]

 

Chemical properties & mechanism: CoA has a long, flexible chain terminating in a sulfhydryl group (SH, a.k.a. thiol) (Figure 7). This group forms an energy-rich thioester bond with acyl groups, thus activating them for the following reactions. For example, in pyruvate dehydrogenase the activation of the acetyl group derived from pyruvate facilitates its entry into the Krebs cycle, where it is fully oxidized to CO2 while producing much energy. Similarly, CoA-activation of fatty acids facilitates their degradation-oxidation to acetyl-CoA units, which are then further degraded-oxidezed to CO2 while releasing much energy.

Figure 7

Figure 7. The molecular structure of coenzyme A and the thioester bond it forms in acetyl-CoA.

Pyridoxal Phosphate (PLP)

Source: vitamin B6 (pyridoxine) (Figure 8, right).

Figure 8

Figure 8. The molecular structure of PLP and vitamin B6.

Physiological importance:

  • Amino acid metabolism.
  • Synthesis of ceramide (a sphingolipid).
  • Synthesis of the neurotransmitters serotonin, dopamine, epinephrine, & norepinephrine.
  • Synthesis of the local mediator histamine.
  • Synthesis of porphyrins (e.g. heme), and therefore of hemoglobin & myoglobin.
  • Breakdown of glycogen (storage form of glucose in animals)

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Chemical properties: PLP has a positively charged pyridinium ring (Figure 8, left), which acts as an electron sink similarly to the thiazolium ring of TDP. This allows PLP to compromise adjacent covalent bonds in the substrate when the two bind to each other.

 

Biochemical reactions: transamination, decarboxylation, racemization, beta/gamma elimination of α-amino acids (Figure 9). The respective enzymes include transaminases, decarboxylases, aldolases, and dehydratases.

Figure 9

Figure 9. Types of chemical reactions involving PLP.

Enzymes (examples):

  • Amino transferases [amino acid breakdown]
  • Glycogen phosphorylase [glycogen breakdown]
  • Serine dehydratase [feeding serine’s breakdown product to gluconeogenesis]
  • Aminolevulinic acid synthase [synthesis of porphyrins]

 

Mechanism (transamination):

In transamination, an amino group is transferred from an amino acid to a keto acid, turning the latter into an amino acid. Thus, the bond that is broken/formed in the reaction is C-N.

Figure 10

Figure 10. Transamination of amino acids

The enzymes that catalyze these reactions, aminotransferases (a.k.a. transaminases), use PLP to facilitate the breakdown of a C-N bond in the substrate and forming it in the product. The steps of transamination are as follows:

  1. An amino acid binds to the enzyme’s active site.
  2. PLP, which is normally bound to a lysine residue in the enzyme via a Schiff base (internal aldimine), detaches from the lysine and forms an equivalent bond with the amino acid’s NH3 group (external aldimine) (Figure 11 step 1).
  3. PLP (an electron sink) polarizes the Ca-NH3 bond, leading to the deprotonation of Ca (Figure 11 step 2). Cα becomes a carbanion, but subsequent electronic rearrangements involving PLP and the substrate render Cα electrophilic (Figure 11 step 3).
  4. Nucleophilic attack of a water molecule on the electrophilic Cα lead to the breaking the Ca-NH3 bond and release of the remaining a-keto acid (Figure 11 step 4).

Figure 11

Figure 11. Individual steps of transamination.

 

Biotin

Biochemical reaction: carboxylation (Figure 12).

Figure 12

Figure 12. Carboxylation of pyruvate

Physiological importance: glucose production, amino acid, lipid metabolism,

Enzymes (examples):

  • Pyruvate carboxylase [gluconeogenesis] (Figure 12).
  • Propionyl-CoA carboxylase [conversion of propionyl-CoA from odd-chain fatty acids, cholesterol and some amino acids to glucose, via succinyl-CoA].
  • Acetyl-CoA carboxylase [fatty acid synthesis].
  • β-methylcrotonyl-CoA carboxylase [amino acid catabolism].

 

Chemical structure: biotin is composed of a ureido ring (the active part) fused to a valeric acid-substituted tetrahydrothiophene ring.

Figure 13

Figure 13. The molecular structure of biotin

 

Mechanism

The role of biotin is to mediate the transfer of an activated carboxyl group (created from bicarbonate and ATP), to another molecule (i.e. the co-substrate). It does that using its ureido group (Figure 13), which attacks the activated carboxyl and then polarizes its carbon atom is it can be further attacked by the co-substrate. The steps are as follows:

  1. An attack of bicarbonate’s O1 oxygen on ATP generates carboxy-phosphate, the activated form of bicarbonate (Figure 14, step 1).
  2. Carboxy-phosphate is unstable and breaks down to CO2 and PO43-. The latter acts as a base, abstracting biotin’s N1’ proton, which turns N1’ into a good nucleophile (Figure 14, steps 2+3).
  3. Biotin’s N1’ attacks the CO2 group and binds to it covalently (Figure 14, step 4).
  4. The bond with biotin renders the carbon of CO2 electrophilic, allowing an attack on it by an oxygen atom of the co-substrate (e.g. pyruvate) (not shown). As a result, CO2 breaks apart from biotin and binds to the co-substrate.

Figure 14

Figure 14. The mechanism of CO2 activation by ATP and biotin.

(Source: JBC 284:11690-7)

 

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Cobalamin (co-enzyme B12)

Source: vitamin B12

Physiological importance:

  • Lipid, amino acid & nucleotide metabolism.
  • DNA synthesis –> blood cells production in the bone marrow.
  • Keeping methylmalonate levels low –> stable myelin –> functional nervous system

Deficiency-associated disease: megaloblastic anemias (e.g. pernicious anemia, which results from malabsorption of B12) – only when there is also folic acid deficiency

Chemical structure: co-enzyme B12 consists of cobalt (CO3+) bound to a substituted corrin ring and an alkyl group (either adenosyl or methyl) (Figure 15).

Figure 15

Figure 15. The structure or co-enzyme B12

It is formed by attack of cobalt on the 5’ carbon of cobalamine (Figure 16):

Figure 16

Figure 16. Formation of co-enzyme B12 from cobalamine.

Examples:

  • Methylmalonyl-CoA mutase [(i) conversion of propionyl-CoA from odd-chain fatty acids, cholesterol and some amino acids to succinyl-CoA and from there to glucose via gluconeogenesis. (ii) keeping the levels of methylmalonate (a known myelin destabilizer) low].
  • Methionine synthase [(i) methionine synthesis from homocysteine (ii) regeneration of tetrahydrofolate, which is important for nucleotide synthesis].

 

Biochemical reactions:

  1. Intramolecular rearrangements – reactions that involve position change of a chemical group with a hydrogen atom on an adjacent carbon, without mixing it with the solution’s hydrogen atoms (Figure 17).
  2. Methyl group transfer from one molecule to another.

Figure 17

Figure 17. Molecular rearrangement catalyzed by co-enzyme B12

 

Mechanism (molecular rearrangements, Figure 18):

  1. The cobalt-C5’ covalent bond is weak, and its dissociation produces a C5’ radical.
  2. The C5’ radical abstracts a hydrogen atom (H∙) from the substrate’s carbon atom, turning it into a radical.
  3. The substituent of the carbon adjacent to the newly form radical switches place to the latter.
  4. The newly formed radical abstract the hydrogen atom (H∙) back from co-enzyme B12, thus completing the rearrangement.

Figure 18        

Figure 18. Mechanism of co-enzyme B12

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Tetrahydrofolate (THF)

Source: Folic acid (vitamin B9).

Figure 19

Figure 19. The molecular structure of folic acid.

 

Physiological importance (Figure 20):

  • DNA/RNA biosynthesis – needed especially for rapidly dividing cells, e.g. blood cells, and also during pregnancy & infancy.
  • Amino acid metabolism (methionine, serine, glycine).
  • Signaling (synthesis of the transmitter nitric oxide).
  • Keeping low homocysteine levels (risk factor for cardiovascular diseases)

Figure 20

Figure 20. Processes involving THF

 

Deficiency-associated diseasemegaloblastic anemia, birth defects (during pregnancy), cardiovascular disease (via homocysteine).

Causes for deficiency (mnemonic: A FOLIC DROP):
Alcoholism
Folic acid antagonists
Oral contraceptives
Low dietary intake
Infection with Giardia
Celiac sprue
Dilatin
Relative folate deficiency
Old
Pregnant

Biochemical reactions: single-carbon unit transfer (methyl, formyl, formaldehyde).

Examples:

  • Thymidylate synthase [dTMP biosynthesis (Figure 21)].
  • Glycinamide ribotide transformylase [purine nucleotides biosynthesis (Figure 21a, step 3)].
  • Aminoimidazole carboxamide ribotide transformylase [purine nucleotides biosynthesis (Figure 21a, step 10)].
  • Methionine synthase [conversion of homocysteine to methionine].
  • Serine hydroymethyl transferase [conversion of serine to glycine (Figure 21b)].

Figure 21

Figure 21. THF-mediated synthesis of dTMP

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Figure 21a

Figure 21a. Involvement of THF in purine nucleotide biosynthesis

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Figure 21b

Figure 21b. THF-mediated conversion of serine to glycine

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Mechanism:

Folic acid is a donor of single-carbon units, needed for the various biosynthetic steps of nucleotides. The single-carbon units appear in the form of formate (in N10-formyl-THF and N5,N10-methenyl-THF, Figure 21), and formaldehyde (in N5,N10-methylene-THF and N5-methyl-THF). These are essentially the cell’s supply of formate and formaldehyde, kept in a relatively innocuous form as a THF adduct until needed.

Figure 22

Figure 22. Two active forms of THF

Clinical importance:

  • THF is important for keeping low level of homocysteine (a risk factor for heart attacks and strokes).
  • DHFR (the THF-regenerating enzyme) is a prime target for anti-cancer drugs, e.g. methotrexate (Figure 23).

Figure 23

Figure 23. Regeneration of THF by DHFR

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