Nucleosol

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Editor-In-Chief: Henry A. Hoff

Overview

Inside the nuclear membrane, including attached to the inner layer of this membrane, are a variety of substances serving special purposes. Depending on conditions, for a time, some of these compose the nucleosol, some compose the nucleohyaloplasm, and still others compose the nucleoplasm. Those substances and the special conditions present, even if temporary, in water can be the nucleosol.

Introduction

Generally, in chemistry a fluid suspension of a colloidal solid in a liquid is referred to as a sol. Whereas, a solution is a liquid mixture of a minor component (the solute) distributed uniformly within the major component (the solvent). A plasm is a formative or formed material; i.e., something molded. Usually a formed material keeps it shape once the mold is removed. Should something be glassy or transparent it can be said to be hyaloid. Whether a fluid is molded or liquid is often a matter of viscosity and whether a fluid is transparent, translucent, or opaque is often a matter of absorption.

Water

In the kinetic theory of gases (such as water vapor) there is a correlation between average energy and temperature:

E_av = 3/2 kT with E_av = 1/2 mv_av².

⇒ v_av² = 3kT/m.

For a water molecule m = 18 Da, or 2.9913 x 10^-23 gmolecule^-1.

⇒ v_rms = √3kT/m = √3·1.382x10^-23 J/K·306 K/(0.018 kg/6.022x10²³) = 651 ms^-1 at 33°C. v_rms is the root mean square velocity.

However, water is a liquid, not a gas. For example, v_rms (O₂) in air at 25°C is 482.1 ms^-1. As a liquid much of the available kinetic energy is expressed through additional degrees of freedom. Some of this energy is in the form of intermolecular bonds. These bonds are a resistance to flow.

Water has a resistance to flow that is considered relatively "thin", having a lower viscosity than other liquids such as vegetable oil. At 25°C, water has a nominal viscosity of 1.0 × 10^-3 Pa∙s and motor oil has a nominal apparent viscosity of 250 × 10^-3 Pa∙s.^[1] Because of its density of <math>\rho</math> = 1 g/cm³ (varies slightly with temperature), and its dynamic viscosity near 1 mPa·s, the viscosity values of water are, to rough precision, all powers of ten:

Dynamic viscosity:

<math>{\mu}</math> = 1 mPa·s = 10^-3 Pa·s = 1 cP = 10^-2 poise

Kinematic viscosity:

<math>{\nu}</math> = 1 cSt = 10^-2 stokes = 1 mm²/s

<math>{\nu}</math> = <math>{\mu}</math>/<math>{\rho}</math>, where <math>{\rho}</math> is the density (kg/m³).

In water

viscosity is independent of pressure (except at very high pressure); and
viscosity tends to fall as temperature increases: from 1.79 cP to 0.28 cP in the temperature range from 0°C to 100°C; see temperature dependence of liquid viscosity for more details.

The viscosity of water is 8.94 × 10⁻⁴ Pa·s or 8.94 × 10⁻³ dyn·s/cm² or 10⁻¹ cP at about 25 °C.
As a function of temperature T (K): μ(Pa·s) = A × 10^B/(T−C)
where A=2.414 × 10⁻⁵ Pa·s ; B = 247.8 K ; and C = 140 K.

Whereas, for a gas such as air, the viscosity is much lower and also depends mostly on temperature. At 15.0 °C, the viscosity of air is 1.78 × 10⁻⁵ kg/(m·s) or 1.78 × 10⁻⁴ cP. One can get the viscosity of air as a function of temperature from the Gas Viscosity Calculator.

Viscous flow in amorphous materials such as water is a thermally activated process:^[2]

μ = <math>\A\cdot e^{Q_L/RT},</math>

where Q_L is the activation energy in the liquid state, T is temperature, R is the molar gas constant and A is approximately a constant.

With

where H_m is the enthalpy of motion of the broken hydrogen bonds, then Q_L may yield the average speed of a water molecule at the temperature, T.

The enthalpy of vaporization for water at 25°C is 44 kJmol^-1. The enthalpy of vaporization can be viewed as the energy required to overcome the intermolecular interactions in water. The molecules in liquid water are held together by relatively strong hydrogen bonds. But care must be taken, however, when using enthalpies of vaporization to measure the strength of intermolecular forces, as these forces may persist to an extent in the gas phase (as is the case with hydrogen fluoride), and so the calculated value of the bond strength will be too low. With water the enthalpy of vaporization is larger than the available kinetic energy suggested by the ideal gas law:

E_av = 3/2 kT with E_av = 1/2 mv_av².

The average speeds of translation for various small molecules having the same kinetic energy as a water molecule, when water is at 500 nms^-1, m = 18 Da, are P_i at 200 nms^-1, m = 96 Da, adenosine (Ado) at 100 nms^-1, m = 267 Da, and EC 3.1.3.5 at 6 nms^-1, m = 140 kDa (homodimer), for the reaction:

Ado + P_i <=> H₂O + AMP,

although EC 3.1.3.5 (70 kDa) may not occur within the nucleosol. But EC 3.1.3.5 NT5C1A cytosolic 5'-nucleotidase 1A, m = 41 kDa^[3] can, with 82 kDa as a homodimer.

Miscible molecules

Miscible molecules such as O₂, CO₂, N₂, and NH₃ occur in any bodily fluid. These molecules are mixed into the liquid, but not turned into ions. Water contains only 1/20 parts O₂. N₂ mixes into the bloodstream and body fats.

Inorganic ions

Relative to the outside of a cell, the concentration of Ca²⁺ is low.^[4] In addition to sodium and potassium ions the nucleosol also contains Mg²⁺^[5]. Some of these magnesium ions are associated with incoming ribonucleoside triphosphate (NTP) as they enter the catalytic center for transcription by RNA polymerase (RNAP) II.^[5] The remaining typical ions found in any cytosol include chloride and bicarbonate.^[6]

Intranuclear posttranscriptional modifications such as mRNA editing convert cytidine to uridine within some mRNA.^[7] This conversion by enzyme EC 3.5.4.5 though infrequent releases ammonia^[8] or produces ammonium (NH₄⁺) in solution. This enzyme is Zn²⁺ dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion (OH^-) that performs a nucleophilic attack on the substrate.^[9]

Cells also maintain an intracellular iron ion (Fe²⁺) homeostasis.^[10] Cu²⁺ serves as a cofactor.^[11] Iron homeostasis involves interconversions of Fe²⁺ with Fe³⁺.

When a nucleotide is incorporated into a growing DNA or RNA strand by a polymerase, pyrophosphate (PP_i) is released. The pyrophosphate anion has the structure P₂O₇⁴⁻, and is an acid anhydride of phosphate. It is unstable in aqueous solution and in the absence of enzymic catalysis hydrolyzes extremely slowly into inorganic phosphate HPO₄²⁻ (orthophosphate, P_i) in all but highly acidic media.^[12]

Enzyme EC 3.6.1.1 catalyzes the hydrolysis of PP_i to P_i:

PP_i + H₂O <=> 2 P_i.

The enzyme is Mg²⁺ binding, occurs in the cytosol, has a 33 kDa form, and no NLS. The enzymes of EC 3.6.1.1, in general, exist as homooligomers.

Carbohydrates

Of the carbohydrates, monosaccharides and oligosaccharides are water soluble. Polysaccharides on the other hand tend to be insoluble in water. As to alcohols, there are two opposing solubility trends: the tendency of the polar OH to promote solubility in water, and of the carbon chain to resist it. Thus, methanol, ethanol, and propanol are miscible in water because the hydroxyl group wins out over the short carbon chain. Butanol, with a four-carbon chain, is moderately soluble because of a balance between the two trends. Alcohols of five or more carbons (pentanol and higher) are effectively insoluble in water because of the hydrocarbon chain's dominance.

Fatty acids

Short chain carboxylic acids such as formic acid and acetic acid are miscible with water and dissociate to form reasonably strong acids (pK_a 3.77 and 4.76, respectively). Longer-chain fatty acids do not show a great change in pK_a. Nonanoic acid, for example, has a pK_a of 4.96. However, as the chain length increases the solubility of the fatty acids in water decreases very rapidly, so that the longer-chain fatty acids have very little effect on the pH of a solution.

When the body uses stored fat as a source of energy, glycerol and fatty acids are released into the bloodstream. The glycerol component can be converted to glucose by the liver and provides energy for cellular metabolism.

Amino acids

The average mass range for amino acids: 75 - 222 Da. By comparison a water molecule is 18 Da. In addition to the proteinogenic standard amino acids, there are a number of other amino acids (aa) involved in the synthesis of the proteinogenic aa: citrulline (Cit), cystathionine (Cth), homocysteine (Hcy), ornithine (Orn), sarcosine (Sar) and taurine (Tau), for example. As Tau does not contain a carboxyl group it is not an aa, but since in its place it does contain a sulfonate group, it may be called an amino sulfonic acid.

Nucleobases

Purine (Pur) 120 Da is not a protein. The purines are the most widely distributed naturally occurring nitrogen-containing heterocycle.^[13] The purine nucleobases include adenine (A) 135 Da, hypoxanthine (Hx) 136 Da, guanine (G) 151 Da, and xanthine (Xan) 152 Da. The pyrimidines include pyrimidine (Pyr) 80 Da, also a heterocycle and naturally occurring, cytosine (C) 111 Da, uracil (U) 112 Da, thymine (T) 126 Da, and queuine (Q) 275 Da.

Nucleosides

Nucleosides are glycosylamines, a nucleobase linked to a ribose or deoxyribose ring. Examples include purines: adenosine (Ado) 267 Da, guanosine (Guo) 283 Da, and inosine (Ino) 268 Da, and pyrimidines: cytidine (Cyd) 243 Da, thymidine (Thd) 242 Da, uridine (Urd) 244 Da, and queuosine (Quo) 409 Da. When the nucleobase is attached to deoxyribose, a 'd' is placed in front of the abbreviation, e.g., dCyd is deoxycytidine 227 Da and the molar mass decreases by one oxygen from Cyd.

Nucleotides

Nucleotides such as orotidine 5'-monophosphate (OMP) range in size from 176 Da (OMP) to 523 Da (GTP). The purine nucleotides involved in RNA or DNA synthesis include: inosine monophosphate (IMP), adenosine triphosphate (ATP), and guanosine triphosphate (GTP). The pyrimidine nucleotides involved include OMP, cytidine triphosphate (CTP), uridine triphosphate (UTP), and thymidine triphosphate (TTP) for DNA in place of UTP. Although rare, higher phosphates do occur such as adenosine tetraphosphate (Ap4) 587 Da. The deoxyribonucleotides have a 'd' in front, like dCTP, except for the thymidine deoxyribonucleotides.

Cofactors

Many cofactors are involved in the synthesis of amino acids and nucleotides. They range in size from ascorbic acid (ASA) 176 Da and biotin (BIO) 244 Da, which are vitamins, to nicotinamide adenine dinucleotide phosphate (NADP) 744 Da and flavin adenine dinucleotide (FAD) 785 Da.

One of the coenzymes essential for the synthesis of amino acids is nicotinamide adenine dinucleotide (NAD) 663 Da. Besides assembling NAD⁺ de novo from simple amino acid precursors, cells also salvage preformed compounds containing nicotinamide. The three natural compounds containing the nicotinamide ring and used in these salvage metabolic pathways are nicotinic acid (Na), nicotinamide (Nam) and nicotinamide riboside (NR).^[14] These compounds are also produced within cells, when the nicotinamide group is released from NAD⁺ in ADP-ribose transfer reactions. Indeed, the enzymes involved in these salvage pathways appear to be concentrated in the cell nucleus, which may compensate for the high level of reactions that consume NAD⁺ in this organelle.^[15] Nicotinamide mononucleotide adenylyl transferase 1 (NMNAT1) (EC 2.7.7.1) catalyzes a key step of NAD synthesis.^[16] It has a nuclear localization signal (NLS).^[16] NMNAT1 may be a substrate for nuclear kinases.^[16]

Peptides

Peptides are short polymers formed from the linking, in a defined order, of α-amino acids. Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and polypeptides/proteins are long. The digestion of dietary proteins produces dipeptides which are absorbed more rapidly than aa. A dipeptide is a molecule consisting of two amino acids joined by a single peptide bond. Examples of dipeptides include carnosine (Car) 244 Da, of the amino acids β-alanine (β-Ala) and histidine (His), homocarnosine (Hcn) 258 Da consisting of γ-aminobutyric acid (GABA) and His, and anserine (Ans) 240 Da.

Oligopeptides

Some tripeptides and tetrapeptides are synthesized in humans. Oligopeptides can range up to 40 aa (9 kDa) generally.

Small proteins (polypeptides)

Due to the size limitation of the nuclear pore, these polypeptides would range from 9 kDa to <70 kDa and not need or have a NLS. For example, emerin 18 kDa (no NLS) mediates inner nuclear membrane anchorage to the nuclear lamina, regulates the flux of beta-catenin into the nucleus, and interacts with nuclear actin.^[17]^[18]^[19]

On the other hand, LEMD1 (20.3 kDa) is involved in the glutamine (Gln) metabolic process^[20] and has a NLS.^[21]

Many of the polypeptides are enzymes including peptidases and kinases.

Proteases

Carnosinase occurs as EC 3.4.13.3 (Xaa-His dipeptidase) with Zn²⁺ as cofactor, 3.4.13.18 (cytosol nonspecific dipeptidase) with Zn²⁺ as cofactor and Mn²⁺ activation, and 3.4.13.20 (beta-Ala-His dipeptidase), activated by Cd²⁺ and citrate, catalyzing the reaction

Car + H₂O <=> His + β-Ala.

It is intracellular to the cytosol and can occur in 14 kDa, 35 kDa, and 44 kDa sizes, often forming a homodimer. As a nonspecific dipeptidase, it degrades a number of dipeptides including Car^[22], Ans and Hcn^[22] as EC 3.4.13.3 and EC 3.4.13.20 per the reaction:

Hcn + H₂O <=> γ-aminobutyric acid (GABA) + His.

Oligopeptides can be degraded by aminopeptidases such as EC 3.4.11.6 19-68 kDa forms (intracellular to the cytosol) with Zn²⁺ as cofactor and activation by Cl^- per the reactions:

oligopeptide (n) + H₂O <=> Lys + oligopeptide (n-1)

oligopeptide (n) + H₂O <=> Arg + oligopeptide (n-1).

Synthases

Enzymes EC 2.3.1.37 (cofactor: pyridoxal phosphate, PLP) aminolevulinate, delta-, synthase 1 (ALAS1) and aminolevulinate, delta-, synthase 2 (ALAS2) anabolically synthesize glycine (Gly) from the amino acid 5-amino-4-oxovaleric acid (ALA) in the two-step reaction:

5-aminolevulinate (C₅H₉NO₃) (ALA) + CO₂ <=> 2-amino-3-oxoadipate (C₆H₉NO₅)

+

2-amino-3-oxoadipate + CoA (C₂₁H₃₆N₇O₁₆P₃S) <=> succinyl-CoA (C₂₅H₄₀N₇O₁₉P₃S) + Gly

=

5-aminolevulinate + CoA + CO₂ <=> succinyl-CoA + Gly

The mRNA for ALAS1 is 82 kDa, the intracellular precursor is a homodimer of 71 kDa, and the mitochondrial mature protein is 65 kDa. But, ALAS1 also occurs in a 30 kDa form.^[23]

CTP synthase EC 6.3.4.2 is the final step in the de novo synthesis of CTP from UTP. As a monomer 67 kDa or dimer it is inactive because three monomers contribute to ligand binding at the active site.^[24] The active form is a homotetramer (a dimer of dimers), with no NLS, intracellular to the cytosol,^[24]^[25] for the following reactions.

UTP + Gln + ATP + H₂O <=> CTP + Glu + ADP + P_i

ATP + UTP + NH₃ <=> ADP + P_i + CTP

The reactions

2 ATP + HCO₃^- + NH₃ <=> 2 ADP + P_i + carbamoyl phosphate (multistep)^[26]

Gln + H₂O <=> Glu + NH₃^[27]

2 ADP + P_i + Glu + carbamoyl phosphate <=> 2 ATP + Gln + HCO₃^- + H₂O^[28]

are catalyzed by EC 6.3.5.5 carbamoyl-phosphate synthase II (CAD). It has no NLS, occurs as a homohexamer, uses Zn²⁺ as a cofactor and is intracellular to the nucleus.^[29] It does occur in a 22 kDa form.^[30]

Kinases

EC 3.6.1.5 (cofactor: Ca²⁺) catalyzes the following reactions:

AMP + P_i <=> ADP + H₂O

AMP + 2 P_i <=> ATP + 2 H₂O

ADP + P_i <=> ATP + H₂O

CMP + P_i <=> CDP + H₂O

CMP + 2 P_i <=> CTP + 2 H₂O

CDP + P_i <=> CTP + H₂O

GMP + P_i <=> GDP + H₂O

GMP + 2 P_i <=> GTP + 2 H₂O

GDP + P_i <=> GTP + H₂O

UMP + P_i <=> UDP + H₂O

UMP + 2 P_i <=> UTP + 2 H₂O

UDP + P_i <=> UTP + H₂O

Ca²⁺ or Mg²⁺ can serve as activating ions. ENTPD1 (CD39) is a 56 kDa protein.^[31] CD39 associates with RanBPM (RANBP9).^[32] RANBP9 (90 kDa)^[33] binds Ran, a small GTP binding protein that is essential for the translocation of RNA and proteins through the nuclear pore complex.^[34] RanBPM localizes in the nucleus and cytoplasm,^[32] but RanBPM has no NLS. CANT1 (EC 3.6.1.6 and 3.6.1.5) 49 kDa^[35] catalyzes similar reactions:

a nucleotide + P_i <=> a nucleoside diphosphate + H₂O,

also acting on IDP, GDP, UDP and on D-ribose 5-diphosphate.^[36] ENTPD7 (EC 3.6.1.-) occurs in the mouse nucleus.^[37]

Enzymes 2.4.2.7 adenine phosphoribosyltransferase (APRT) 19.4 kDa (forms a dimer, 38.8 kDa) is intracellular (cytoplasm)^[38] and 2.4.2.8 hypoxanthine phosphoribosyltransferase 1 (HPRT1) 24 kDa (forms a tetramer, 96 kDa) is intracellular (cytosolic)^[39] catalyze the following reaction:

Adenine + 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) <=> AMP + PP_i

Neither APRT nor HPRT1 has a NLS. APRT is a dimer in solution at pH 6.5, but a monomer at pH 8.0, and like HPRT1 needs Mg²⁺, or Mn²⁺.^[40]

Enzymes EC 3.6.1.5 ATP pyrophosphohydrolase, ADPase^[41]/ADP synthase^[42] ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1) 56 kDa catalyzes the conversion of AMP into ADP (see below). Cofactor: Ca²⁺.^[43] Ca²⁺ or Mg²⁺ can serve as activating ions. Also acts on ADP, and on other nucleoside triphosphates and diphosphates.^[43]

AMP + P_i <=> ADP + H₂O

Enzymes EC 2.7.4.6 nucleoside-diphosphate kinases A, B, C, D (NDKA-D) catalyzes the following reaction inside the nucleosol as it is intracellular (nucleus)^[44] and each gene is translated as a 7-11 kDa particle^[45]. However, these kinases exist either as tetramers (28-44 kDa) in bacteria or hexamers (42-66 kDa).^[46] Once the hexamer has formed the particle may be too big to pass through the nuclear pores. NDKA has been shown to mediate transcription, associate with a promoter region of a gene, and be a member of the SET or INHAT complex which can modulate gene expression.^[47] Nucleoside-diphosphate kinase does form nuclear and cytoplasmic hexamers.^[48] NDKA-D do not have a NLS.

ADP + GTP <=> ATP + GDP

Transaminases

In catabolic transamination, with PLP as a cofactor, EC 2.6.1.2 transfers the amine from glutamic acid (glutamate) (Glu) to alanine (Ala) via a two step reaction:

PLP + Glu <=> pyridoxamine monophosphate (PMP) + α-ketoglutarate (2-oxoglutarate)

+

PMP + pyruvate <=> PLP + Ala

=

pyruvate + Glu <=> Ala + 2-oxoglutarate.

Although this enzyme has several different names, e.g., alanine transaminase, glutamic-pyruvate transaminase (GPT), or alanine aminotransferase, it can occur as a monomer of 55 kDa or homodimer of 101 kDa, and as either a cytosolic (GPT1), or mitochondrial form (GPT2).

Synthetases

The reactions

ATP + Glu + NH₃ (or NH₄⁺) <=> ADP + P_i + Gln

ATP + Asp + NH₄⁺ <=> ADP + P_i + Asn

ATP + Asp + NH₄⁺ <=> AMP + PP_i + Asn

are catalyzed by the enzyme EC 6.3.1.2 glutamine synthetase (GS), glutamine-ammonia ligase (GLUL). GLUL 42 kDa is intracellular, occurs as a homooctamer,^[49] also as 12 kDa and 22 kDa forms,^[50] and complexes with phosphate, ADP, and Mn²⁺.

Histone pools in the nucleosol

Histones H2A, H2B, H3, and H4 are in the nucleosol, and H2B, H3, and H4 are also in the cytosol.^[51]

Enzyme activity

EC 2.4.1.101 (UDP-N-acetylglucosaminyl transferase) occurs and is active in the nuclesol.^[52]

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikipedia.

References

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↑ "Apropos IpiRecord: IPI00413533".
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↑ "Apropos IpiRecord: IPI00012048".
↑ "NCBI Conserved Domains cd04413: NDPK_I".
↑ Curtis CD, Likhite VS, McLeod IX, Yates JR, Narulli AM (2007). "Interaction of the Tumor Metastasis Suppressor Nonmetastatic Protein 23 Homologue H1 and Estrogen Receptor {alpha} Alters Estrogen-Responsive Gene Expression". Cancer Res. 67 (21): 10600–7. doi:1158/0008-5472.CAN-07-0055 Check |doi= value (help). PMID 17975005. Unknown parameter |month= ignored (help)
↑ Klouckova I, Hrncirova P, Mechref Y, Arnold RJ, Li TK, McBride WJ, Novotny MV (2006). "Changes in liver protein abundance in inbred alcohol-preferring rats due to chronic alcohol exposure, as measured through a proteomics approach". Proteomics. 6 (10): 3060–74. doi:0.1002/pmic.200500725 Check |doi= value (help). PMID 16619309. Unknown parameter |month= ignored (help)
↑ "GENATLAS : GENE Database GLUL".
↑ "Apropos IpiRecord: IPI00830929".
↑ Tsvetkov S, Ivanova E, Djondjurov L (1989). "The pool of histones in the nucleosol and cytosol of proliferating Friend cells is small, uneven and chasable". Biochem J. 264 (3): 785–91. PMID 2619716. Unknown parameter |month= ignored (help)
↑ Marshall S, Okuyama R (2004). "Differential effects of vanadate on UDP-N-acetylglucosaminyl transferase activity derived from cytosol and nucleosol". Biochem Biophys Res Commun. 318 (4): 911–5. PMID 15147958. Unknown parameter |month= ignored (help)