Conformational Dynamics of Proteins
 

GAUSSIAN NETWORK MODEL

Dependence of Effective Force Constants on Protein Size


Figure 1. Force constant vs. number of residues. Open circles refer to the proteins listed in Table 1.
 


Figure 2. Force constant normalized with respect to the resolution of the examined structure, as a function of n.
The ordinate represents the GNM force constant divided by the resolution, shortly denoted as g
 


Figure 3. Same as Figure 2, on a logarithmic scale (both axes). The line indicates the best fitting curve obeying the power law: g = 22.8 n^(-1.22), with a correlation coefficient of 0.86, excluding the two terminal points
 

Table 1.The PDB code of the proteins, their resolutions, number of residues and computed force constant g

PDB Code

n

Resolution (Å)

g (kcal/mol.Å 2)

g Resolution

1crn

46

1.5

1.71

1.14

4rxn

54

2

0.847

0.423

5pti

58

1.8

0.810

0.270

5ebx

62

2

0.995

0.249

1r69

63

2

0.647

0.129

1sn3

65

1.8

1.12

0.187

2utg

70

1.64

1.35

0.193

1hoe

74

2

0.559

0.0699

451c

82

1.6

1.17

0.130

2ci2

83

2

0.683

0.0683

2gn5

87

2.3

0.817

0.0743

1aba

8

1.45

0.946

0.0789

256b

106

1.4

0.845

0.0650

1fkf

107

1.7

1.13

0.0809

2cdv

107

1.8

1.65

0.110

1paz

120

1.55

0.743

0.0465

1alc

122

1.7

0.573

0.0337

9rsa

124

1.8

1.15

0.0637

2aza

129

1.8

0.513

0.0270

1eca

136

1.4

1.41

0.0705

1hds

141

1.98

0.929

0.0442

2sod

151

2.0

2.93

0.133

3lzm

164

1.7

0.848

0.0369

9wga

171

1.8

1.17

0.0489

1rbp

175

2.0

0.583

0.0233

1cc5

178

2.5

0.642

0.0247

2ltn

181

1.7

1.69

0.0626

8dfr

186

1.7

0.424

0.0151

3adk

194

2.1

1.67

0.0577

2stv

195

2.5

0.695

0.0232

3gap

208

2.5

1.26

0.0405

9pap

212

1.65

0.883

0.0276

3cla

219

1.75

1.05

0.0317

3sgb

242

1.8

0.934

0.0275

2cab

260

2.0

0.879

0.0251

2sec

275

1.8

1.05

0.0293

2sni

275.

2.1

0.924

0.0250

8atc

310

2.5

0.508

0.0134

1fnr

314

2.2

0.866

0.0222

6tmn

316

1.6

1.03

0.0257

2ts1

319

2.3

0.975

0.0238

4pep

326

1.8

0.638

0.0152

2liv

344

2.4

1.47

0.0342

8adh

374

2.4

0.555

0.0126

1wsy

393

2.5

0.867

0.0193

2ccp

414

2.2

0.702

0.0153

5cts

433

1.9

1.27

0.0271

8cat

500

2.5

0.854

0.0178

1cdk

740

2.0

0.988

0.0200


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