Principles of Protein Structure - H. Schulz 1982

Mechanisms of polypeptide chain folding and association
Structural domains
Structural classes

Structural domains can be classified according to their Secondary Structure. Known domain structures can be divided into the five classes listed in Table 5.2, based on their type, Abundance, and secondary structure Organization [249, 250]. Of greatest interest are domains consisting of a single type of secondary structure. Among these, a-helical domains can be expected to undergo the simplest folding process. Helix formation apparently occurs at the early stage of folding, after which the only remaining task is the energetic favorable packing of the a-helical cylinders.

All-ß-Structure domains (Class 2) contain antiparallel ß-structures, which provide a strong correlation between residues close in the chain (Fig. 5.15, a). They are characterized by a high degree of order. Less ordered structures belong to Class 3, which comprises domains where a- and ß-structures are segregated along the peptide chain. Class 4 is formed predominantly by parallel ß-structures in the center of the domains surrounded by a-helices, so that a- and ß-structures tend to alternate along the chain. The Rossmann fold (Fig. 5.12, b) belongs to this class. Domains lacking a pronounced secondary structure are grouped into Class 5.

Table 5.2 Domain structure and Structural classes of Globular Proteins a

Structural class

Fraction of the globular protein occupied by the structural domain

Number of residues in the domain

Protein

Number of domains in the globular protein

Number of domain-connecting chains

№ 1

a-helices only

Entire protein

104

Cytochrome c [271—273]

1

»

158

TMV coat protein [180, 218]

1

»

108

Parvalbumin [59]

1

»

~ 145

Hemoglobin [188, 274—276]

1

»

153

Myoglobin [185, 277]

1

»

~ 120

Hemerythrin [216, 217]

1

»

51

Insulin [259]

1

»

29

Glucagon [278]

1

C-terminus

111

Papain [279]

2

1

»

160

Thermolysin [280]

2

1

»

90

T4 Lysozyme [241]

2

1

N- and C-termini

~100,

Tyr-tRNA synthetase [221]

3

~ 100


№ 2

Almost exclusively

β-structure

Entire protein

237

Concanavalin A [281, 282]

1





»

127

Proalbumin [206, 283]

1

»

54

Rubredoxin [284, 285]

1

»

151

Superoxide dismutase [286, 800]

1

»

62

Erabutoxin b [287]

1

Entire protein

113

Subtilisin inhibitor [798]

1

N-terminus

110

Papain [279]

2

(1)

N- and C-termini

128, 114

Chymotrypsin [18]

2

1

»

110, 119

Elastase [243]

2

1

»

107, 116

Trypsin [244, 245]

2

1

»

80, 106

Proteinase B [246]

2

1

»

175, 145

Acid protease [288—290]

2

1

N-terminus

175

Alcohol dehydrogenase [234]

2

1

Entire protein

~ 110

Immunoglobulin [291—294]

2, 4

1

№ 3

a-Helix and ß-structure segregated along the chain

Entire protein

258

Carbonic anhydrase [295, 296]

85

Calf Liver cytochrome b5 [297, 298] High-potential iron-sulfur protein [299]

1

»

85

1

»

129

Hen egg-white lysozyme [260, 300]

1

56

Pancreatic trypsin inhibitor [269]

1

Entire protein

124

Ribonuclease [39, 301, 302]

1

»

149

Staphylococcal nuclease [242]

1

»

~330

Bacteriochlorophyll protein [303]

1

N-terminus

156

Thermolysin [280]

1

(1)

74

T4 lysozyme [241]

2

C-terminus

150

Lactate dehydrogenase [232]

2

(1)

170

s-Malate dehydrogenase [233]

2

1

118

Glutathione reductase [124]

2

1

Entire protein

194

Adenylate kinase [186]

3

№ 4

a-Helix and ß-structure,

alternating along the chain

1

»

307

Carboxypeptidase [43]

1

140

Flavodoxin [237, 238]

1

275

Subtilisin [239, 240]

1

»

108

Thioredoxin [304]

1

Entire protein



»

247

Triosephosphate isomerase [305]

1

~ 240

Bacterial aldolase [306]

1

~ 230

Phosphoglycerate mutase [307]

1

159

Dihydrofolate Reductase [308]

1

N-terminus

181

Lactate dehydrogenase [232]

2

(1)

»

~ 150

s-Malate dehydrogenase [233]

2

(1)

C-terminus

199

Alcohol dehydrogenase [234]

2

(1)

N- and C-termini

147, 187

Glyceraldehyde-3-phosphate dehydrogenase [230, 231]

2

1

»

~150, ~150

L-Arabinose-binding protein [309]

2

(1)

»

~180, ~175

Phosphoglycerate kinase [235, 310, 311]

2

»

~250, ~150

Pyruvate kinase [80, 312]

3

»

~130, ~130

Rhodanese [257, 799]

2

»

~360, ~150

Glucosephosphate isomerase [313]

2

~230, ~230

Hexokinase [261]

2

N-terminus and central region

210, 134

Glutathione reductase [124]

3





Central region

~200

Tyr-tRNA synthetase [221]

3

№ 5

Neither a-helix nor ß-sheet

Entire protein

54

Ferredoxin [314]

1

»

124

Phospholipase [315]

1

»

41

Wheat germ agglutinin [316]

4

1








If the chain topology has not yet been confirmed by Amino Acid Sequence data, the number of domain-connecting chains in multidomain proteins is omitted. The number of chains is denoted as (I) if about ten residues at the N- or C-termini of the chain overlap with another domain. Classes 3 and 4 are also referred to as a+β and a/ß, respectively [249].

Obviously, such a Classification can be useful in interpreting the folding process. This task becomes more complex as the class number increases, i.e., as the structural regularity of the chain decreases.



Last update: 06/08/2026

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