СПИРАЛЬНЫЕ ПАРАМЕТРЫ РЕГУЛЯРНЫХπ-СПИРАЛЕЙ В БЕЛКАХ (ЧАСТЬ 2) Текст научной статьи по специальности «Медицинские технологии»

УДК 579.519.6

doi 10.18101/2306-2363-2016-4-17-25

© D. Batkhishig, B. Mijiddorj, P. Enkhbayar

HELICAL PARAMETERS OF REGULAR п-HELICES IN PROTEINS

(Part 2)

The a-helix, 310-helix, п-helix and co-helix have been observed in protein structures. They account for 32% of residues, 4%, 0.3% and 0.2%, respectively. However, these percentages depend on resolution of solved structures and method for assignment of secondary structures. May 2016, culled Protein Data Bank (PDB) data set, containing 2901 protein chains with less than 25% sequence identity and < 1.6Л resolution (R-value < 0.25), was used in this analysis. Secondary structure assignments are performed by DSSP, STRIDE and SECSTR for п-helices. Helical parameters-pitch, residues per turn, radius, handedness and p = rmsd/(N-1)1/2 for п-helices are determined by HELFIT program. p-Value, estimates helical regularity and all п-helices with p <0.10Л, were identified as regular. Helical parameters of protein п-helices are compared with those of canonical п-helices and other types of protein helices.

Keywords: 310-helix, a-helix, п-helix, helical parameters, regular helix, protein structures, protein chains.

Д. Батхишиг, Б. Муиддорж, П. Энхбаяр

СПИРАЛЬНЫЕ ПАРАМЕТРЫ РЕГУЛЯРНЫХ п-СПИРАЛЕЙ В БЕЛКАХ (Часть 2)

а-Спираль, 310-спираль, п-спираль и о-спираль наблюдались в белковых структурах. Они составляют 32% от остатков, 4%, 0,3% и 0,2%, соответственно. Однако эти проценты зависят от разрешения решаемых структур и способу присвоения вторичных структур. Возможно 2016, из отобранного набора в данных банк белков (PDB), содержащих 2901 белковые цепи с менее чем 25% идентичности последовательности и < 1.6Л разрешающей способности (R-значения < 0.25), использовать в этом анализе. Вторичные задания структуры выполняются DSSP, STRIDE и SECSTR для п-спиралей. Спиральные параметры шага, остатки на оборот, радиусы, хиральности и р = RMSD/(N-1)1/2 для p-спиралей определяются программой HELFIT. р-Значения, оценивающие спиральную регулярность и все п -спиралей с р < 0.10Л, были идентифицированы как регулярные. Спиральные параметры белка p-спиралей сравнивались с данными канонических p-спиралей и других типов белковых спиралей.

Ключевые слова: 310-спиралей, а-спиралей, п-спираль, спиральные параметры, регулярные спирали, белковые структуры, белковые цепи.

Introduction

Helix is one of two main types of secondary structures in proteins. Helices are usually designated as in based on the number of residues per turn (i) and the number of atoms in the ring joined by the backbone hydrogen bond (n) [1]. Pauling and Corey first hypothesized the a-helix (3.6i3) and the y-helix (5.li7) structures [2]. Donohue later considered the possibility of other types of helices (2.2, 3ю, 4.3M and 4.416) [3]. Low and Baybutt also suggested the possibility of the 4.4i6-helix or п-helix [3]. The main stabilizing factor for helical structures in polypeptides is re-

peated hydrogen bonds between main chain carbonyl oxygen (C=O) and amide hydrogen (NH) groups with the a-helix characterized by an (/ ^ /+4) pattern, the 310 and the n-helix by repealing (/ ^ /+3) and (/ ^ /+5) hydrogen bonds, respectively [4].

There are several programs perform assignments of secondary structures based on three-dimensional (3D) atomic coordinates of proteins [4-6]. Among these, DSSP [4] and STRIDE [5] are the most widely used [7]. DSSP identifies helices based on the repeating (/W+n) hydrogen bonds with corresponding to n of 3, 4 and 5 for 310, a- and n-helices, respectively [4, 8]. STRIDE uses both hydrogen bonds and main chain dihedral angles to define secondary structures [5]. DSSP program identified only 9 unique n-helices from the database of more than 6000 of proteins [9]. Fodje and Karadaghi defined 116 n-helices using their home made program, SECSTR, from the database of 932 high resolution 3D structures of proteins [7].

These different results can be explained by the following two reasons: 1) Number of solved 3D structures was insufficient by this time 2) Programs to assign of secondary structures use different methods.

We studied helical parameters of protein helices with HELFIT program and compared with the parameters of canonical rc-helices.

Materials and Methods

Composition of database

The 16 May 2016 culled PDB data set, containing 2969 protein chains with less than 20% sequence identity and resolution < 1.6 A (R-value < 0.25), was used in this analysis.

DSSP program

DSSP performs secondary structure assignments by the bonding energy £<-0.5 kcal/mol between C=O of residue / and N-H residue n (/ ^ /+n). The optimal hydrogen bonding energy for mainchain-mainchain N—H--O hydrogen bonds Em < -3 kcal/mol. Hydrogen bond energy depends on both electrostatic interaction N—H-••O of atoms and of hydrogen bonds angle 6 [4].

STRIDE program

STRIDE program is designed for protein secondary structure assignment from 3D atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information [7]. The hydrogen bond energy Ehb is calculated using the empirical energy function derived from the analysis of experimental data on hydrogen bond geometries in crystal structures of amino acids in polypeptide chains [10].

SECSTR program

SECSTR is a new addition to the DSSP program that is dedicated to identifying n-helices, which were seldom assigned by older versions of DSSP and STRIDE [7]. The secondary structure assignment methods based on hydrogen bond assignments (DSSP, STRIDE, and SECSTR) produced nearly identical assignments, with more than to 90% [6].

HELFIT program

HELFIT enables to calculate simultaneously all five of the helix parameters with high accuracy. The minimum number of data points required for the analysis is only four. HELFIT also calculates a parameter, p = RMSD/(N-1)12, which estimates the regularity of helical structures independent of the number of data points, where RMSD is the root mean square distance from the best-fit helix to data points and N is the number of data points [11]. Results and Discussion

We identified 27, 22 and 340 n-helices from 2901 high resolution protein structures by DSSP, STRIDE and SECSTR programs, respectively. All n-helices are divided into two groups, regular and irregular, withp-value: p < 0.10 A regular and p > 0.10 A irregular. 7 of 27, 5 of 22, and 76 of 340 helices are grouped as regular by the HELFIT program. In order to compare protein n-helices with the canonical n-helices the only parameters of regular n-helices are used for the further analysis (Table 1).

Table 1

Helical parameters of 86 regular n-helices in proteins identified by DSSP, STRIDE and SECSTR program

PDB ID Chain_Po sition P (A) n Az (A)4 r (A) Vc (A3)" P (A) Identified Program

1DJ0 A 81-87 5.01 4.18 1.20 2.58 25.06 0.10 SECSTR

1DK8 A 242249 5.12 4.36 1.17 2.69 26.70 0.10 SECSTR

1ELK A 95-101 5.24 4.42 1.19 2.70 27.15 0.10 SECSTR

1JET A 301308 4.82 4.44 1.09 2.80 26.74 0.09 SECSTR

1KJQ A 119125 5.10 4.30 1.19 2.67 26.56 0.09 SECSTR

1KK O A 199205 4.99 4.53 1.10 2.81 27.33 0.09 DSSP, STRIDE, SECSTR

1NU Y A_1276-1282 5.30 4.64 1.14 2.87 29.56 0.10 SECSTR

1RK6 A_386-393 5.30 4.47 1.19 2.80 29.20 0.06 DSSP

1RK6 A_387-393 5.14 4.41 1.17 2.74 27.49 0.04 STRIDE

1RK6 A_384-393 5.22 4.37 1.19 2.71 27.56 0.06 SECSTR

1W5 R A_58-64 5.17 4.37 1.18 2.73 27.70 0.08 SECSTR

1XG0 A 105111 5.32 4.55 1.17 2.84 29.63 0.10 SECSTR

1XG K A 266272 5.02 4.31 1.16 2.70 26.67 0.07 SECSTR

2BF D A 109-115± 5.20 4.50 1.16 2.80 28.46 0.10 SECSTR

2CI1 A 51-57 5.12 4.33 1.18 2.68 26.68 0.09 SECSTR

2DPL A_68-74 5.17 4.42 1.17 2.77 28.20 0.03 SECSTR

2GZS A 163169 5.31 4.53 1.17 2.83 29.49 0.09 SECSTR

P (A) n Az (A)b r (A) Vc (A3)" P (A) Identified Program

5.15 4.21 1.22 2.62 26.38 0.09 SECSTR

5.15 4.42 1.17 2.75 27.68 0.07 SECSTR

5.13 4.48 1.15 2.79 28.00 0.08 SECSTR

5.15 4.32 1.19 2.71 27.51 0.08 SECSTR

5.18 4.38 1.18 2.73 27.69 0.08 SECSTR

5.24 4.42 1.19 2.77 28.58 0.09 SECSTR

5.29 4.52 1.17 2.81 29.03 0.10 SECSTR

5.17 4.39 1.18 2.76 28.18 0.02 DSSP

5.09 4.42 1.15 2.75 27.36 0.06 DSSP

5.06 4.42 1.14 2.78 27.80 0.05 STRIDE

5.08 4.42 1.15 2.75 27.31 0.06 SECSTR

5.25 4.49 1.17 2.77 28.19 0.09 SECSTR

5.27 4.00 1.32 2.79 32.22 0.09 SECSTR

5.36 4.55 1.18 2.81 29.22 0.10 SECSTR

5.20 4.34 1.20 2.70 27.44 0.08 SECSTR

5.11 4.23 1.21 2.62 26.05 0.10 SECSTR

5.11 4.32 1.18 2.70 27.09 0.06 SECSTR

5.07 4.40 1.15 2.77 27.78 0.08 SECSTR

5.28 4.44 1.19 2.75 28.25 0.09 SECSTR

5.16 4.45 1.16 2.80 28.56 0.04 SECSTR

4.97 4.29 1.16 2.72 26.93 0.07 SECSTR

5.13 4.62 1.11 2.88 28.93 0.10 SECSTR

5.49 4.41 1.24 2.74 29.36 0.08 SECSTR

5.25 4.54 1.16 2.83 29.10 0.06 SECSTR

5.18 4.44 1.17 2.77 28.12 0.10 SECSTR

5.30 4.50 1.18 2.81 29.22 0.08 SECSTR

5.17 4.43 1.17 2.77 28.13 0.06 SECSTR

5.24 4.45 1.18 2.76 28.18 0.09 SECSTR

5.29 4.45 1.19 2.77 28.66 0.05 SECSTR

5.14 4.41 1.17 2.75 27.69 0.10 SECSTR

5.04 4.25 1.19 2.68 26.76 0.10 DSSP

PDB ID

Chain_Po sition

2H1V

2JIS 200А

2P51

2P6 W 2PB D

2POF

2PY

Q

2PY X

2PY X

2PY X

2RB K

2VL

A

2WQ

F

A_264-274

A_28-35

A_424-

430

A_207-213

A_154-160

A_88-94

A_37-43 B_61-67

A_232-239

A_232-

238

A_232-

239

A_122-129

A_68-77 A_59-65

2XR A_300-

Y 306

2Y53 A 48-54

3A0Y A 723-

729

3BH A 128-

Q 134

3H9C A_382-

391

3IT3 A_56-63

3OAJ A 24-30

3OCJ A 253-

259

3OY A_227-

V 233

3PB6 X_93-99

3PJP A 1334-

1340

3Q28 A 280-

286

3RRI A_22-28

3S5 A_692-

M 698

3T4L A 168-

174

3VE A 437-

N 443

3WA X_297-

2 303

PDB ID

Chain_Po sition

P (A) n Az (A)4 r (A) Vc (A3)" P (A) Identified Program

5.22 4.50 1.16 2.82 28.98 0.08 SECSTR

5.18 4.28 1.21 2.65 26.70 0.10 SECSTR

5.22 4.42 1.18 2.76 28.26 0.09 SECSTR

5.06 4.35 1.16 2.76 27.84 0.05 SECSTR

5.22 5.07 1.03 2.72 23.93 0.06 SECSTR

5.11 4.38 1.17 2.75 27.72 0.07 SECSTR

5.25 4.55 1.15 2.81 28.62 0.09 SECSTR

4.99 4.32 1.16 2.73 27.05 0.09 SECSTR

5.10 4.39 1.16 2.75 27.60 0.10 SECSTR

5.36 4.14 1.29 2.59 27.28 0.07 SECSTR

5.02 4.35 1.15 2.72 26.82 0.09 SECSTR

5.19 4.46 1.16 2.76 27.85 0.06 DSSP

5.14 4.46 1.15 2.80 28.39 0.07 STRIDE

5.16 4.44 1.16 2.77 28.01 0.05 SECSTR

5.13 4.36 1.18 2.73 27.55 0.08 DSSP

5.12 4.40 1.16 2.74 27.45 0.09 STRIDE

5.21 4.38 1.19 2.71 27.44 0.09 SECSTR

5.29 4.53 1.17 2.85 29.80 0.10 SECSTR

5.28 4.46 1.18 2.78 28.74 0.09 SECSTR

4.86 4.47 1.09 2.81 26.97 0.09 SECSTR

5.08 4.53 1.12 2.84 28.42 0.09 SECSTR

5.11 4.38 1.17 2.74 27.52 0.09 SECSTR

5.07 4.54 1.12 2.85 28.50 0.07 SECSTR

5.23 4.53 1.15 2.81 28.64 0.08 SECSTR

5.18 4.38 1.18 2.73 27.69 0.06 SECSTR

5.15 4.33 1.19 2.69 27.04 0.08 SECSTR

5.30 4.45 1.19 2.74 28.09 0.10 SECSTR

5.17 4.49 1.15 2.79 28.16 0.09 SECSTR

5.22 4.40 1.19 2.73 27.78 0.09 SECSTR

5.29 4.53 1.17 2.80 28.76 0.10 SECSTR

3ZB O

4AY O

4B1Y

4BR

C

4CB U

A_94-100

A_122-128

B_88-94

A_359-

365

A 89-95

4CD5 A 248-

254

4CD5 A_350-

356

4DJA A_305-

311

4DJA A 405-

412

4ES A 137-

M 143

4EZI A 128-

135

4GV A 231-

F 239

4GV A 232-

F 238

4GV A 229-

F 239

4I3G A 257-

264

4I3G A 257-

263

4I3G A 253-

264

4JA8 A_66-72

4LRT A 267-

273

4ME A 192-

2 198

4QB3 A_66-72

4R75 A 311-

318

4U9H L_127-

133

4W7 A_373-

L 379

4WRI A 65-71

4XE A 120-

M 126

4XFJ A_68-74

4XQ7 A 217-

223

4Z5S A 108-

115

4ZG A 115-

W 121

PDB ID Chain_Po sition P (A) n Az (A)b r (A) Vc (A3)" P (A) Identified Program

5A0Y A 314324 5.09 4.46 1.14 2.77 27.51 0.10 SECSTR

5AZ B A 203210 5.15 4.41 1.17 2.74 27.54 0.09 SECSTR

5BSR A_240-247 5.12 4.33 1.18 2.68 26.68 0.10 SECSTR

5DA W A_89-95 5.32 4.37 1.22 2.72 28.30 0.09 SECSTR

5DP2 A 143149 5.18 4.44 1.17 2.78 28.33 0.06 SECSTR

5E8X A_442-448 5.09 4.35 1.17 2.74 27.60 0.08 SECSTR

5EJ8 A 485491 5.22 4.55 1.15 2.81 28.46 0.10 SECSTR

5HZ7 A 280286 5.25 4.49 1.17 2.80 28.80 0.08 SECSTR

Average 5.17±0 4.42±0 1.17±0 2.75±0 27.89± 0.08±0

.11 .13 .04 .06 1.09 .02

Canonical n-helix 5.16 4.40 1.15 2.68 25.9 -

a Voronoi volume (Vc=n r Az); Helix rise per residue Az=P/n;

Total of 88 regular n-helices are 7, 5 and 76 identified by DSSP, STRIDE and SECSTR program respectively. The n-helix is identified at position 199-205 of A chain in 1KKO protein by the three programs [12-18].

Helix radius and Voronoi volume of real n-helices are larger than that of canonical n-helix. The other helix parameters are close to the parameters of canonical n-helix. Average length is 7.47 residues and length is in range of 7-12 residues (Table 2).

Table 2

Average of helical parameters for regular n-helices in proteins and standard

deviations

Average <P> (A) <n> <Az>(A) <r> (A) <VC>(A3) <p> (A)

n-helices 5. 13±0. 4 ,41±0. 1.16±0. 2.76±0. 27.75±0. 0.07±0.

(DSSP) 10 09 03 04 78 03

n-helices 5. 09±0. 4 ,44±0. 1.15±0. 2.77±0. 27.69±0. 0.07±0.

(STRIDE) 06 05 02 03 38 02

n-helices 5. 17±0. 4 ,42±0. 1.17±0. 2.75±0. 27.90±1. 0.08±0.

(SECSTR) 11 13 04 06 13 02

Standard deviations of helical parameters for n-helices identified by SECSTR program are larger than DSSP and STRIDE programs. Also, average values of the helix radius r and number of residue per turn n are approximate to each for the three programs.

B)

ISO

-ISO

C)

ISO

-ISO

с 6 О с* О

> 'Jv

ISO

-180

ISO

Fig. The Ramachandran-map of regular n-helices in proteins. The 9, y angles are indicated in panels which regular n-helices identified by A) DSSP, B) STRIDE and C) SECSTR, respectively. The abscissa is 9; the ordinate axis is y. The 9, y of residues at Nc and Cc are not shown.

Average dihedral angles of regular n-helices were determined at each for DSSP (-77°±14°, -50°±11°), STRIDE (-77°±15°, -51°±12°) and SECSTR (-81°±18°, -44°±21°) programs. The average values of backbone dihedral angles (9, y) of all regular n-helices observed were found to be (9, y)=(-81°, -45°) with standard deviations (o9, oy)=(17°, 20°). The average of dihedral angle is larger than canonical n-helix (-57°, -70°). The 9, y angles of regular n-helices are located on an allowed regions for other residues except for glycine, were removed from the calculation (Fig.).

Conclusion

• 2901 3D structures of high resolution protein structures were downloaded from Protein Data Bank (PDB) and there are 389 n-helices. In average, every protein contains 0.13 n-helices.

• All n-helices are divided into two groups, regular and irregular. 89 n-helices are regular among the total of 389 n-helices, 4.37%. Helix parameters of all regular n-helices are used for further analysis.

• Radii of all n-helices and Voronoi volume are larger than that of canonical n-helices and all the helical parameters are comparable with those of canonical helices.

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Batkhishig D., Department of Physics, School of Mathematics and Natural Science, Mongolian National University of Education, Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia Ulaanbaatar, Mongolia, E-mail: [email protected]. mn

Mijiddorj B., Laboratory of Bioinformatics and Systems Biology, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia.

Enkhbayar P., Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia, E-mail: [email protected]

Батхишиг Д., Отделение физики, школа математики и естественных наук, Монгольский национальный педагогический университет, лаборатория биоинформатики и системной биологии, Отделение информационных и компьютерных наук, школа инженерных и прикладных наук, Национальный университет Монголии, Монголия, Улан-Батор, E-mail: [email protected]

Mijiddorj B., лаборатория биоинформатики и системной биологии, Отделение информационных и компьютерных наук, школа инженерных и прикладных наук, Национальный университет Монголии, Монголия, Улан-Батор

Энхбаяр П., лаборатория биоинформатики и системной биологии, Отделение информационных и компьютерных наук, школа инженерных и прикладных наук, Национальный университет Монголии, Монголия, Улан-Батор, E-mail: [email protected]. mn