二十种氨基酸的结构和功能
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20种氨基酸的结构与功能特点
Glycine
1. Gly存在于Pr中一般都有作用，因其容易destabilize Pr
2. Contact point of α helices (prior to N-terminus, 因为易形成turn)
3. C-cap of α helices
4. Flattening of antiparallel β sheets
5. Interior of parallel barrels
6. Nucleotide binding motifs (GxGxxG)
Proline
1. 虽然疏水，但是经常在Pr表面，因为易形成turn
2. Little loss of entropy upon folding; rigid linkers; help to stabilize Pr
3. Helix starter (If internal to helices, bend ~30o, because 2 H-bonds lost)
4. Φ near -60o
5. No N-H for H-bonds
6. Steric interference of the ring
Turns a) Type I
b) Type II (Pro at position 2)
c) Type VI cis-Pro turn (at position 3；两种：Type VIa和Type VIb)
a、b两种85％，c占15％
Proline经常出现在α helices的第一圈（但不是第一个aa），原因：
a) 第1圈helix没法形成H-bond，Proline正好合适
b) 第1圈不存在空间位阻，Proline有位阻正好合适
c) Proline的环正好可以bend the helix
Cysteine
1. -SH虽然极性，但很少在Pr表面
2. free -SH都在胞内，disulfide bonds都在胞外
3. ligand -SH (metal)：Fe、Zn、Cu
Alanine
1. "Alanine Scanning" mutagenesis：Ala不会打破原有结构
2. generic "default"
3. common in α helices
Valine, Methionine, Leucine, Isoleucine
1. Hydrophobic packing in Pr interior
2. Common rotamers
3. β sheets:
a) continuous hydrophobic sheet
b) preference for β-branched side chains (Val, Ile>Leu, Met)
4. α helices:
a) interdigitation of side chains
b) preference for long, unbranced side chains (Met>Leu>Ile>Val)
Histidine (pKa ~6.5)
1. Rare and most always functional, 不是为了Pr的结构而存在
2. Active sites' residue
3. Ligand for metals
4. Usually beried
5. pKa at physiological pH (regulatable)
Phenylalanine
Hydrophobic interior
Tyrosine
1. Inside/outside, no preference （一方面有疏水苯环，另一方面有亲水羟基）
2. Phosphorylatable
Tryptophan
Relatively hydrophobic，所以relatively interior
Serine
1. Good for creating turns: "helix starter" (50% of helices begin with N, S, D)
2. Active site nucleophile
3. Phosphorylation
4. O-linked glycosylation
Threonine
More hydrophobic; Thr也可以Ser的3、4两项
Asparagine
1. Pseudoturns：only Asn
2. Helix starter (N, S, D；都是非常极性)
3. N-linked glycosylation
Glutamine
1. Longer chain distinguishes it from asparagine
2. Preferences for helices
Aspartate, Glutamate (pKa 4)
1. Similar to Asn and Gln but negatively charged
2. Metal ion binding residues; Active sites' residues；Salt bridges
3. Asp is helix starter (N, S, D)
Lysine (pKa 10), Arginine (pKa 12)
1. Great surface residues: side chain has both aliphatic and ionic character
既亲水（末端正电），又疏水（长碳链）
2. DNA-binding residues；Salt bridges
3. C-terminus of α helices
4. Lys:
mobile (great solubilizer): Lys → disordered → solubilize
5. Arg:
a) more hydrophobic → more structured & ordered than Lys
b) hydrogen bond scaffold (planer guanidinium group)
Glycine
1. Gly存在于Pr中一般都有作用，因其容易destabilize Pr
2. Contact point of α helices (prior to N-terminus, 因为易形成turn)
3. C-cap of α helices
4. Flattening of antiparallel β sheets
5. Interior of parallel barrels
6. Nucleotide binding motifs (GxGxxG)
Proline
1. 虽然疏水，但是经常在Pr表面，因为易形成turn
2. Little loss of entropy upon folding; rigid linkers; help to stabilize Pr
3. Helix starter (If internal to helices, bend ~30o, because 2 H-bonds lost)
4. Φ near -60o
5. No N-H for H-bonds
6. Steric interference of the ring
Turns a) Type I
b) Type II (Pro at position 2)
c) Type VI cis-Pro turn (at position 3；两种：Type VIa和Type VIb)
a、b两种85％，c占15％
Proline经常出现在α helices的第一圈（但不是第一个aa），原因：
a) 第1圈helix没法形成H-bond，Proline正好合适
b) 第1圈不存在空间位阻，Proline有位阻正好合适
c) Proline的环正好可以bend the helix
Cysteine
1. -SH虽然极性，但很少在Pr表面
2. free -SH都在胞内，disulfide bonds都在胞外
3. ligand -SH (metal)：Fe、Zn、Cu
Alanine
1. "Alanine Scanning" mutagenesis：Ala不会打破原有结构
2. generic "default"
3. common in α helices
Valine, Methionine, Leucine, Isoleucine
1. Hydrophobic packing in Pr interior
2. Common rotamers
3. β sheets:
a) continuous hydrophobic sheet
b) preference for β-branched side chains (Val, Ile>Leu, Met)
4. α helices:
a) interdigitation of side chains
b) preference for long, unbranced side chains (Met>Leu>Ile>Val)
Histidine (pKa ~6.5)
1. Rare and most always functional, 不是为了Pr的结构而存在
2. Active sites' residue
3. Ligand for metals
4. Usually beried
5. pKa at physiological pH (regulatable)
Phenylalanine
Hydrophobic interior
Tyrosine
1. Inside/outside, no preference （一方面有疏水苯环，另一方面有亲水羟基）
2. Phosphorylatable
Tryptophan
Relatively hydrophobic，所以relatively interior
Serine
1. Good for creating turns: "helix starter" (50% of helices begin with N, S, D)
2. Active site nucleophile
3. Phosphorylation
4. O-linked glycosylation
Threonine
More hydrophobic; Thr也可以Ser的3、4两项
Asparagine
1. Pseudoturns：only Asn
2. Helix starter (N, S, D；都是非常极性)
3. N-linked glycosylation
Glutamine
1. Longer chain distinguishes it from asparagine
2. Preferences for helices
Aspartate, Glutamate (pKa 4)
1. Similar to Asn and Gln but negatively charged
2. Metal ion binding residues; Active sites' residues；Salt bridges
3. Asp is helix starter (N, S, D)
Lysine (pKa 10), Arginine (pKa 12)
1. Great surface residues: side chain has both aliphatic and ionic character
既亲水（末端正电），又疏水（长碳链）
2. DNA-binding residues；Salt bridges
3. C-terminus of α helices
4. Lys:
mobile (great solubilizer): Lys → disordered → solubilize
5. Arg:
a) more hydrophobic → more structured & ordered than Lys
b) hydrogen bond scaffold (planer guanidinium group)
