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BMC Bioinformatics

Open Access

DBBP: database of binding pairs in protein-nucleic acid interactions

BMC Bioinformatics201415(Suppl 15):S5

https://doi.org/10.1186/1471-2105-15-S15-S5

Published: 3 December 2014

Abstract

Background

Interaction of proteins with other molecules plays an important role in many biological activities. As many structures of protein-DNA complexes and protein-RNA complexes have been determined in the past years, several databases have been constructed to provide structure data of the complexes. However, the information on the binding sites between proteins and nucleic acids is not readily available from the structure data since the data consists mostly of the three-dimensional coordinates of the atoms in the complexes.

Results

We analyzed the huge amount of structure data for the hydrogen bonding interactions between proteins and nucleic acids and developed a database called DBBP (D ataB ase of B inding P airs in protein-nucleic acid interactions, http://bclab.inha.ac.kr/dbbp). DBBP contains 44,955 hydrogen bonds (H-bonds) of protein-DNA interactions and 77,947 H-bonds of protein-RNA interactions.

Conclusions

Analysis of the huge amount of structure data of protein-nucleic acid complexes is labor-intensive, yet provides useful information for studying protein-nucleic acid interactions. DBBP provides the detailed information of hydrogen-bonding interactions between proteins and nucleic acids at various levels from the atomic level to the residue level. The binding information can be used as a valuable resource for developing a computational method aiming at predicting new binding sites in proteins or nucleic acids.

Background

Protein-nucleic acid interactions play an important role in many biological activities. Site-specific DNA-binding proteins or transcription factors (TFs) play important roles in gene regulations by forming protein complexes [1]. These protein-DNA complexes may bind alone or in combination near the genes whose expression they control [2]. For example, DNA-binding proteins may regulate the expression of a target gene [1], so protein-DNA interactions are important for DNA replication, transcription and gene regulations in general.

Protein-RNA interactions also have important roles in a wide variety of gene expression [3]. For instance, ribonucleoprotein particles (RNPs) bind to RNA in the post-transcriptional regulation of gene expression [4], and tRNAs bind to aminoacyl-tRNA synthetases to properly translate the genetic code into amino acids [5]. As protein and RNA mutually interact, RNA-binding proteins are essential molecules in degradation, localization, regulating RNA splicing, RNA metabolism, stability, translation, and transport [6]. Therefore, identification of amino acids involved in DNA/RNA binding or (ribo)nucleotides involved in amino acid binding is important for understanding of the mechanism of gene regulations.

As the number of structures of protein-DNA/RNA complexes that have been resolved has been increased plentifully for the past few years, a huge amount of structure data is available at several databases [710]. However, the data on the binding sites between proteins and nucleic acids is not readily available from the structure data, which consist mostly of the three-dimensional coordinates of the atoms in the complexes. A recent database called the Protein-RNA Interface Database (PRIDB) [9] provides the information on protein-RNA interfaces by showing interacting amino acids and ribonucleotides in the primary sequences. However, it does not provide the binding sites on the interacting partners of the amino acids and ribonucleotides in protein-RNA interfaces.

In this study we performed wide analysis of the structures of protein-DNA/RNA complexes and built a database called DBBP (D ataB ase of B inding P airs in protein-nucleic acid interactions). The database shows hydrogen-bonding interactions between proteins and nucleic acids at an atomic level, which is not readily available in any other databases, including the Protein Data Bank (PDB) [11]. The binding pairs of hydrogen bonds provided by the database will help researchers determine DNA (or RNA) binding sites in proteins and protein binding sites in DNA or RNA molecules. It can also be used as a valuable resource for developing a computational method aiming at predicting new binding sites in proteins or nucleic acids. The rest of the paper presents the structure and interface of the database.

Materials and methods

Protein-DNA/RNA complexes

The protein-DNA/RNA complexes determined by X-ray crystallography were selected from PDB. As of February, 2013 there were 2,568 protein-DNA complexes and 1,355 protein-RNA complexes in PDB. After extracting complexes with a resolution of 3.0 Å or better, 2,138 protein-DNA complexes (called the DS1 data set) and 651 protein-RNA complexes (the DS2 data set) remained.

Binding sites in protein-nucleic acid interactions

Different studies [9, 1214] have defined slightly different criteria for a binding site in protein-nucleic acid interactions. For example, in RNABindR [15, 16] and BindN [17] an amino acid with an atom within a distance of 5 Å from any other atom of a ribonucleotide was considered to be an RNA-binding amino acid.

As for the criteria for a binding site between proteins and nucleic acids, we use a hydrogen bond (H-bond), which is stricter than the distance criteria. The locations of hydrogen atoms (H) were inferred from the surrounding atoms since hydrogen atoms are invisible in purely X-ray-derived structures. H-bonds between proteins and nucleic acids were identified by finding all proximal atom pairs between H-bond donors (D) and acceptors (A) that satisfy the following the geometric criteria: (1) the hydrogen-acceptor (H-A) distance < 2.5 Å, (2) the donor-hydrogen-acceptor (D-H-A) angle > 90°, (3) the contacts with the donor-acceptor (D-A) distance < 3.9 Å, (4) H-A-AA angle > 90°, where AA is an acceptor antecedent. These are the most commonly used criteria for H bonds. In particular, the criteria of H-A distance < 2.5 Å and D-H-A angle > 90° are essential for H bonds [18]. If there is no H-bond within a protein-nucleic acid complex, we eliminated the complex from the data sets of DS1 and DS2. As a result, we gathered 2,068 protein-DNA complexes (DS3) and 637 protein-RNA complexes (DS4).

As an example, Figure 1 shows three H-bonds between Threonine (Thr224) and Cytosine (C8) in a protein-RNA complex (PDB ID: 4F3T) [19]. In protein-RNA interactions, OG1 and N of Threonine can act as a hydrogen donor and OG1 and O of Threonine can act as a hydrogen acceptor. N3, N4, O2′ and O3′ of Cytosine can act as a hydrogen donor and N3, O2, O2′, O3′, O4′, O5′, OP1 and OP2 of Cytosine can act as a hydrogen acceptor. In this example, Cytosine is the 8th nucleotide in RNA chain R and Threonine is the 224th amino acid in protein chain A. OG1 of Threonine donates hydrogen to O2′ of Cytosine, OG1 of Threonine donates hydrogen to O3′ of Cytosine, and O2' of Cytosine donates hydrogen to OG1 of Threonine. Figure 2 shows the structure of the protein-RNA complex (PDB ID: 4F3T).
Figure 1

Three H-bonds between Cytosine (C8) and Threonine (Thr224). Three H-bonds between Cytosine (C8) and Threonine (Thr224) of a protein-RNA complex (PDB ID: 4F3T). O2′ of Cytosine donates hydrogen to OG1 of Threonine. OG1 of Threonine donates hydrogen to O2′ of Cytosine and OG1 of Threonine donates hydrogen to O3′ of Cytosine.

Figure 2

The structure of a protein-RNA complex (PDB ID: 4F3T). The enlarged box shows three hydrogen bonds between Cytosine and Threonine. O2′ donates hydrogen to OG1. OG1 donates hydrogen to O2′ and O3′.

The probability of binding amino acid

Let P (+) be the probability that an amino acid is a binding site and P (−) be the probability that an amino acid is a non-binding site in protein-nucleic acid interactions (Equations 1 and 2).
P ( + ) = DNA/RNA - binding amino acids amino acids in protein - DNA/RNA complexes
(1)
P ( - ) = DNA/RNA - non - binding amino acids amino acids in protein - DNA/RNA complexes
(2)
Then, the conditional probability P(A|+) is the probability that the binding amino acid is A. Likewise, the conditional probability P(A|−) is the probability that the non-binding amino acid is A. Equation 5 is the log-likelihood ratio of P(A|+) and P(A|−).
P ( A | + ) = P ( A + ) P ( + )
(3)
P ( A | - ) = P ( A + ) P ( - )
(4)
l o g - l i k e l i h o o d r a t i o = l o g 2 P ( A | + ) P ( A | - )
(5)

Results and discussion

Hydrogen bonds in protein-nucleic acid interactions

We obtained H-bonds from 2,068 protein-DNA complexes (DS3) and 637 protein-RNA complexes (DS4) using HBPLUS [18, 20] with the H-bond criteria: H A ¯ < 2 . 5 A , DHA > 90°, D A ¯ < 3 . 9 A . There are a total of 44,955 H-bonds in protein-DNA complexes and 77,947 H-bonds in protein-RNA complexes. Table 1 shows the number of atoms, which are occurrences in H-bonds of amino acids. In the 44,955 H-bonds of protein-DNA complexes, there are 41,298 hydrogen donors and 3,657 hydrogen acceptors in amino acids. In the 77,947 H-bonds of protein-RNA complexes, there are 59,796 hydrogen donors and 18,151 hydrogen acceptors in amino acids. Table 2 shows the number of atoms, which are occurrences in H-bonds of (ribo)nucleotides. In the 44,955 H-bonds of protein-DNA complexes, there are 3,657 hydrogen donors and 41,298 hydrogen acceptors in DNAs. In the 77,947 H-bonds of protein-RNA complexes, there are 18,151 hydrogen donors and 59,796 hydrogen acceptors in RNAs.
Table 1

Atoms of amino acids involved in H-bonding interactions with nucleic acids.

  

RNA-protein complex

DNA-protein complex

AA

Atom

Acceptor

Donor

#H-bonds

Acceptor

Donor

#H-bonds

Ala

N

 

1,069

1,653

 

674

808

 

O

567

  

134

  
 

OXT

17

     

Arg

NH2

 

9,252

22,395

 

6,144

13,705

 

NH1

 

7,278

  

4,665

 
 

NE

 

4,011

  

2,191

 
 

N

 

1,388

  

606

 
 

O

455

  

99

  
 

OXT

13

     

Asn

ND2

 

3,268

4,953

 

2349

3,119

 

OD1

934

  

408

  
 

N

 

549

  

261

 
 

O

202

  

101

  

Asp

OD2

1,416

 

2,829

353

 

735

 

OD1

1,183

  

290

  
 

O

178

  

31

  
 

N

 

52

  

61

 

Cys

SG

23

76

125

19

120

215

 

O

24

     
 

N

 

2

  

76

 

Gln

NE2

168

2496

4,468

2

1,593

2,571

 

OE1

1,108

  

363

521

 
 

N

 

480

    
 

O

216

  

92

  

Glu

OE2

1,691

 

3,507

275

 

737

 

OE1

1,315

  

260

  
 

O

193

  

19

  
 

N

 

308

  

183

 

Gly

N

 

1,518

2,699

 

1749

1,902

 

O

1,175

  

153

  
 

OXT

6

     

His

NE2

412

1,454

3,591

30

768

1,254

 

ND1

536

1,014

 

15

327

 
 

N

 

106

  

90

 
 

O

69

  

24

  

Ile

N

 

258

309

 

433

466

 

O

40

  

33

  
 

OXT

11

     

Leu

N

 

507

766

 

362

387

 

O

259

  

25

  

Lys

NZ

 

9,864

  

5,145

6,351

 

N

 

852

11,436

86

1,120

 
 

O

717

     
 

OXT

3

     

Met

SD

105

 

662

15

 

147

 

O

276

  

13

119

 
 

N

 

278

    
 

OXT

3

     

Phe

O

333

 

539

42

 

247

 

N

 

206

  

205

 

Pro

O

161

 

161

28

 

28

Ser

OG

1,179

4,675

6,997

182

3,533

4,741

 

N

 

683

  

958

 
 

O

460

  

68

  

Thr

OG1

1,058

4,406

7,267

158

3,017

4,252

 

O

750

  

132

  
 

N

 

1,053

  

945

 

Trp

NE1

 

532

582

 

358

393

 

OXT

16

     
 

O

14

  

10

  
 

N

 

20

  

25

 

Tyr

OH

597

1,935

2,682

133

1,800

2,511

 

O

93

  

28

  
 

N

 

57

  

550

 

Val

O

174

 

326

36

 

386

 

N

 

151

  

350

 
 

OXT

1

     
  

18,151

59,796

77,947

3,657

41,298

44,955

Table 2

Atoms of nucleotides involved in H-bonding interactions with amino acids.

  

RNA-protein complex

DNA-protein complex

Nucleotide

Atom

Acceptor

Donor

#H-bonds

Acceptor

Donor

#H-bonds

A

N1

402

140

22,103

58

23

10,254

 

N3

1,071

79

 

748

26

 
 

N6

 

1,472

  

621

 
 

N7

505

  

580

  
 

O2'

4,240

4,269

    
 

O3'

1,711

86

 

361

100

 
 

O4'

252

  

276

  
 

O5'

110

  

188

  
 

OP1

1,754

  

4,039

  
 

OP2

6,012

  

3,234

  

C

N3

335

49

16,189

127

3

9,502

 

N4

 

785

  

1,272

 
 

O2

2,556

  

959

  
 

O2'

2,101

2,209

 

1

1

 
 

O3'

1,150

56

 

257

139

 
 

O4'

663

  

209

  
 

O5'

117

  

118

  
 

OP1

5,176

  

3,858

  
 

OP2

992

  

2,558

  

G

N1

547

759

30,350

2

204

14,864

 

N2

 

3,907

  

761

 
 

N3

655

53

 

399

2

 
 

N7

1,660

  

2,238

  
 

O2'

2,047

  

2,383

  
 

O3'

1,031

24

 

438

157

 
 

O4'

450

  

420

  
 

O5'

585

  

197

  
 

O6

2,396

  

2,272

  
 

OP1

10,523

  

4,359

  
 

OP2

3,330

  

3,415

  

U/T

N3

173

386

9,305

29

234

10,335

 

O2

1,561

  

1,165

  
 

O2'

1,310

1,445

    
 

O3'

1,067

49

 

351

114

 
 

O4

1,199

  

796

  
 

O4'

166

  

257

  
 

O5'

45

  

216

  
 

OP1

1,108

  

3,548

  
 

OP2

796

  

3,625

  

59,796

18,151

77,947

41,298

3,657

44,955

If an atom of DNA acts as a hydrogen acceptor, an atom of protein should be a hydrogen donor. Hence, the number of DNA acceptors (41,298) is the same as the number of protein donors (41,298), and the number of DNA donors (3,657) is the same as the number of protein acceptors (3,657). Likewise, the number of RNA acceptors (59,796) is the same as the number of protein donors (59,796) and the number of RNA donors (18,151) is the same as the number of protein acceptors (18,151).

Figure 3 shows RNA-binding amino acids in protein-RNA complexes. Ala, Arg, Glu, Gly, Leu, Lys, and Val are more frequent than others in protein-RNA complexes (Figure 3A). In binding sites with RNA, Arg has the most frequently observed amino acid. Figure 3C shows the log-likelihood ratio (Equation 5) for each amino acid. Amino acids with a positive log-likelihood ratio have a higher chance to bind to RNA than those with a negative log-likelihood ratio. Arg has the highest log-likelihood ratio (1.59), and Val has the lowest log-likelihood ratio (-4.24). Interestingly, Ala has a negative log-likelihood ratio although it is frequently observed in protein-RNA complexes. This is because Ala is rarely observed in binding sites.
Figure 3

RNA-binding amino acids in protein-RNA complexes. (A) Amino acids in the protein-RNA complexes and RNA-binding amino acids. (B) The probability that the binding amino acid is A (P(A|+)) and the probability that non-binding amino acid is A (P(A|−)). (C) The log-likelihood ratio log2(P(A|+)/P(A|−)).

Figure 4 shows DNA-binding amino acids in protein-DNA complexes. Ala, Arg, Glu, Gly, Leu, Lys, Ser, and Val are more frequent than others in protein-DNA complexes (Figure 4A). As in protein-RNA interactions, Arg has the most frequently observed amino acid in the binding sites with DNA.
Figure 4

DNA-binding amino acids in protein-DNA complexes. (A) Amino acids in the protein-DNA complexes and DNA-binding amino acids. (B) The probability that the binding amino acid is A (P(A|+)) and the probability that non-binding amino acid is A (P(A|−)). (C) The log-likelihood ratio log2(P(A|+)/P(A|−)).

Web interface

DBBP shows binding pairs at various levels, from the atomic level to the residue level. When it shows detailed information on H-Bonds, it shows the donors and acceptors of each H-bond. A same type of atom can play a role of hydrogen donor or acceptor depending on the context. We generated XML files for binding sites of protein-DNA/RNA complexes. Users of the database can access the XML file via PDB ID.

Figure 5 shows our XML schema. The BindPartner element has elements and attributes, which are PDB ID, protein sequence (proSeq), protein bond (proBnd), DNA/RNA sequence (dnaSeq, rnaSeq), and DNA/RNA bond (dnaBnd, rnaBnd). DNA/RNA and protein bonds represent binding site '+' and non-binding site '-'. The BindingSite element has attributes, which are PDBID, Acceptor, Acceptor chain, Acceptor index, Acceptor residue, Donor, Donor chain, Donor index, and Donor residue.
Figure 5

The XML schema of the database. XML files were generated for the binding sites in protein-DNA complexes and protein-RNA complexes via the XML schema.

Conclusion

From an extensive analysis of the structure data of protein-DNA/RNA complexes extracted from PDB, we have identified hydrogen bonds (H-bonds). Analysis of the large amount of structure data for H-bonds is labor-intensive, yet provides useful information for studying protein-nucleic acid interactions. The protein-DNA complexes contain 44,955 H-bonds, which have 3,657 hydrogen acceptors (HA) and 41,298 hydrogen donors (HD) in amino acids, and 41,298 HA and 3,657 HD in nucleotides. The protein-RNA complexes contain 77,947 H-bonds, which have 18,151 HA and 59,796 HD in amino acids, and 59,796 HA and 18,151 HD in nucleotides. Using the data of H-bonding interactions, we developed a database called DBBP (D ataB ase of B inding P airs in protein-nucleic acid interactions). DBBP provides the detailed information of H-bonding interactions between proteins and nucleic acids at various levels. Such information is not readily available in any other databases, including PDB, but will help researchers determine DNA (or RNA) binding sites in proteins and protein binding sites in DNA or RNA molecules. It can also be used as a valuable resource for developing a computational method aiming at predicting new binding sites in proteins or nucleic acids. The database is available at http://bclab.inha.ac.kr/dbbp.

Declarations

Acknowledgements

This work was funded by the Ministry of Science, ICT and Future Planning (2012R1A1A3011982) and the Ministry of Education (2010-0020163) of Republic of Korea. The cost of the article was funded by the Ministry of Science, ICT and Future Planning (2012R1A1A3011982).

This article has been published as part of BMC Bioinformatics Volume 15 Supplement 15, 2014: Proceedings of the 2013 International Conference on Intelligent Computing (ICIC 2013). The full contents of the supplement are available online at http://www.biomedcentral.com/bmcbioinformatics/supplements/15/S15.

Authors’ Affiliations

(1)
Institute for Information and Electronics Research, Inha University
(2)
Department of Chemistry, Inha University
(3)
School of Computer Science and Engineering, Inha University

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© Park et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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