Hydrophobic and Hydrophilic Amino Acids

As the building blocks of proteins and peptides, amino acids are essential for peptide synthesis and drug discovery due to their unique characteristics. Hydrophobic and hydrophilic amino acids are two significant classes of amino acids that possess distinct characteristics and can be applied in a variety of ways. In peptide synthesis and drug development, the interplay between hydrophobic and hydrophilic amino acids is essential because it enables the creation of peptides with particular characteristics and roles. Researchers can adjust characteristics including peptide structure, stability, solubility, membrane permeability, and binding affinity by carefully combining hydrophobic and hydrophilic amino acids into peptide sequences.

Hydrophobic Amino Acids

Hydrophobic amino acids, also known as nonpolar amino acids, have side chains composed of carbon and hydrogen atoms, which makes them very soluble in water. These amino acids are typically found inside proteins and help stabilize their core structure. Hydrophobic amino acids can be broadly divided into two more specific categories: aliphatic amino acids and aromatic amino acids.

• Aliphatic Amino Acids

Aliphatic amino acids (glycine, alanine, valine, leucine, isoleucine, and proline) often contain branched hydrocarbon chains, ranging from the simplest glycine to the more complex leucine and valine acid structure. Proline is also classified as an aliphatic amino acid, but due to the cyclization of the hydrocarbon chain and the terminal amine, a unique 5-membered ring structure is formed, which has special properties. Due to the structural rigidity of the proline ring structure, it can significantly change the three-dimensional structure of the protein and often occurs at folding or turning regions in the protein.

• Aromatic Amino Acids

Aromatic amino acids (phenylalanine, tyrosine, and tryptophan) contain aromatic functional groups. They are mostly non-polar and hydrophobic in their structure due to their high carbon/hydrogen content. However, it is worth noting that hydrophobicity and hydrophilicity represent a sliding scale, and different amino acids can have different physical and chemical properties depending on their structure. For example, the presence of hydroxyl groups in tyrosine increases its reactivity and solubility compared to phenylalanine.

Which Amino Acids are Hydrophobic?

• Glycine (Gly, G)

- Molecular weight: 75.07 g/mol

- Characteristics: As the smallest amino acid, glycine has only one hydrogen atom in its side chain. It is precisely because of the small size of its side chain that it makes glycine extremely flexible. It often appears in tightly folded regions of proteins, such as the triple helix structure of collagen, and its flexibility is crucial for the construction of proteins.

• Alanine (Ala, A)

- Molecular weight: 89.09 g/mol

- Characteristics: The side chain of alanine is a methyl group, which is one of the most basic non-polar amino acids and often appears in the α-helical structure of proteins. As one of the more abundant amino acids in proteins, alanine usually provides stability to the protein skeleton and participates in constituting the active center of the enzyme, affecting the substrate specificity of the enzyme.

• Phenylalanine (Phe, F)

- Molecular weight: 165.19 g/mol

- Characteristics: Phenylalanine plays an important role in cell signaling and neurotransmitter synthesis because it contains a benzene ring and is a precursor to many neurotransmitters, including dopamine and epinephrine.

• Proline (Pro, P)

- Molecular weight: 115.13 g/mol

- Characteristics: The side chain of proline forms a ring structure with the amino group, which plays a key role in the folding and stabilization of protein chains. In collagen, it helps maintain the integrity of its triple helix structure.

• Valine (Val, V)

- Molecular weight: 117.15 g/mol

- Characteristics: The chemical name of valine is 2-amino-3-methylbutyric acid. It is a branched-chain amino acid and is an essential amino acid and glycogenic amino acid for the human body. It promotes normal body growth, repairs tissues, regulates blood sugar, and provides needed energy. Isobutyraldehyde can be used as raw material for synthesis.

• Leucine (Leu, L)

- Molecular weight: 131.18 g/mol

- Characteristics: The chemical name of leucine is L-2-amino-4-methylpentanoic acid, which is white crystal or crystalline powder; odorless and slightly bitter in taste. Easily soluble in formic acid, slightly soluble in water, and very slightly soluble in ethanol or ether. Leucine, isoleucine, and valine are all branched-chain amino acids that help promote muscle recovery after training.

• Isoleucine (Ile, I)

- Molecular weight: 131.18 g/mol

- Characteristics: Isoleucine is named α-amino-β-methylvaleric acid and its chemical formula is C₆H₁₃NO₂. It is one of the essential amino acids for human body and a kind of aliphatic neutral amino acid. Soluble in water, slightly soluble in ethanol. Rhomboid leaf-shaped or flaky crystals, bitter taste.

• Tyrosine (Tyr, T)

- Molecular weight: 181.19 g/mol

- Characteristics: The chemical name of tyrosine is 2-amino-3-p-hydroxyphenylpropionic acid. It is an aromatic polar α-amino acid containing phenolic hydroxyl groups and is a white crystalline powder. The relative density is 1.456 (20 ℃), and the isoelectric point is 5.66. It has the ability to absorb ultraviolet rays, has maximum light absorption at a wavelength of 274 nm, and can reduce phosphomolybdic acid-phosphotungstic acid reagent (Forin reagent).

• Tryptophan (Trp, W)

- Molecular weight: 204.23 g/mol

- Characteristics: Tryptophan, also known as β-indolylalanine, is one of the essential amino acids for the human body. Appearance is white or slightly yellow crystals or crystalline powder, odorless and slightly bitter in taste. Tryptophan is an important precursor for auxin biosynthesis in plants, and is also the precursor of 5-hydroxytryptamine, an important neurotransmitter in the human body.

Hydrophilic Amino Acids

Polar, hydrophilic amino acids have side chains that contain polar atoms, such as oxygen or sulfur. The side chains of these amino acids can form hydrogen bonds, which contribute to protein stability and intermolecular interactions. Hydrophilic amino acids can be divided into three main categories: polar uncharged, acidic, and basic functional groups. Many amino acids with hydrophilic R groups can participate in the active site of enzymes. The active site is the part of an enzyme that directly binds to the substrate and carries out the reaction. Protein-derived enzymes contain catalytic groups consisting of amino acid R groups that promote bond formation and degradation. Amino acids that play an important role in the binding specificity of the active site are usually not adjacent to each other in the primary structure, but fold to form the active site when the tertiary structure is created.

• Polar Uncharged Amino Acids

In the polar uncharged species, the side chains contain heteroatoms (oxygen, sulfur, or nitrogen) capable of forming a permanent dipole within the R group. These include the amino acids containing hydroxyl and sulfonate oxygen groups, serine, threonine and cysteine, and the amino acids containing amide, glutamine and asparagine.

• Acidic Amino Acids

Acidic amino acids, such as aspartic acid and glutamic acid, contain carboxyl groups that can donate protons, making them negatively charged at physiological pH. These amino acids play important roles in protein folding and stability as well as enzyme catalysis. The negatively charged side chains of aspartic acid and glutamic acid can interact with positively charged ions or other polar molecules through electrostatic interactions.

• Basic Amino Acids

Basic amino acids contain amino groups that can accept protons, making them positively charged at physiological pH. The two most common basic amino acids are lysine and arginine, which contain amino groups in their side chains. Histidine is another important basic amino acid that can act as a proton donor or acceptor depending on the pH of the environment. These basic amino acids play critical roles in a variety of biological processes, including enzymatic catalysis, protein-protein interactions, and signal transduction.

Which Amino Acids are Hydrophilic?

• Serine (Ser, S)

- Molecular weight: 105.09 g/mol

- Characteristics: Serine plays a vital role in the active site of many enzymes and can participate in substrate binding and catalytic reactions. Its hydroxyl side chain is the target of many phosphorylation reactions that are critical in regulating protein activity and signaling.

• Threonine (Thr, T)

- Molecular weight: 119.12 g/mol

- Characteristics: Similar to serine, the hydroxyl group of threonine is also a target for phosphorylation, and the unique structure of its side chain allows it to play a special role at a specific position in the protein structure, such as in the binding site of an antibody.

• Lysine (Lys, K)

- Molecular weight: 146.19 g/mol

- Characteristics: The amino group at the end of the side chain of lysine is positively charged at physiological pH. The positively charged side chain of lysine is particularly important in nucleic acid-binding proteins because it can interact with the negatively charged phosphate groups of DNA or RNA. It is also involved in post-translational modifications of histones and other proteins, such as acetylation and methylation.

• Glutamic Acid (Glu, E)

- Molecular weight: 147.13 g/mol

- Characteristics: Glutamic acid serves as a key metabolic intermediate, involved in amino acid metabolism and neurotransmitter synthesis. Its negatively charged side chain (containing a carboxyl group that becomes negatively charged upon release of a proton) enables it to play a key catalytic role in the protein's active site.

• Cysteine (Cys, C)

- Molecular weight: 121.16 g/mol

- Characteristics: The sulfur atom of cysteine enables it to form a disulfide bond with another cysteine, thereby stabilizing the three-dimensional structure of the protein. In signal transduction, the oxidation or reduction state of cysteine residues can affect protein activity.

• Glutamine (Gln, Q)

- Molecular weight: 146.15 g/mol

- Characteristics: Glutamine is the amide of glutamic acid. L-Glutamine is a coded amino acid in protein synthesis. It is a non-essential amino acid for mammals and can be converted from glucose in the body. Glutamine is used to treat gastric and duodenal ulcers, gastritis, and hyperacidity, and is also used to improve brain function.

• Aspartic Acid (Asp, D)

- Molecular weight: 133.11 g/mol

- Characteristics: Aspartic acid is an α-amino acid, and its L-isomer is one of the 20 protein amino acids, which is the structural unit of protein. It is an acidic amino acid together with glutamic acid. Aspartate is ubiquitous in biosynthesis. It is the synthetic precursor of amino acids such as lysine, threonine, isoleucine, methionine and purine and pyrimidine bases in organisms. It can serve as a carrier of K⁺ and Mg²⁺ ions to transport electrolytes to the myocardium, thereby improving myocardial contractile function and reducing oxygen consumption.

• Arginine (Arg, R)

- Molecular weight: 174.20 g/mol

- Characteristics: Arginine is an essential amino acid in the human body. It participates in the ornithine cycle in the human body, promotes the formation of urea, and converts ammonia produced in the human body into non-toxic urea through the ornithine cycle. Arginine, histidine, and lysine are basic amino acids.

• Histidine (His, H)

- Molecular weight: 155.16 g/mol

- Characteristics: Histidine is an alpha-amino acid with the chemical formula C₆H₉N₃O₂. In the context of nutrition, histidine is considered an essential amino acid for humans, mainly for children. After adulthood, humans can begin to synthesize histidine on their own. In addition, histidine is also one of the necessary raw materials for the synthesis of some pharmaceutical intermediates, such as the blue copper peptide ghk-cu.

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