Enzyme ResearchVolume 2011 (2011), Article ID 328249, 12 pagesdoi:10.4061/2011/328249

Research Article

Computational Simulations to Predict Creatine Kinase-Associated Factors: Protein-Protein Interaction Studies of Brain and Muscle Types of Creatine Kinases

Wei-Jiang Hu,¹ Sheng-Mei Zhou,² Joshua SungWoo Yang,3,4 and Fan-Guo Meng¹

¹Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China²College of Biology and Chemical Engineering, Jiaxing University, Jiaxing 314001, China³Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea⁴Department of Bioinformatics, University of Sciences & Technology, Daejeon 205-305, Republic of Korea

Received 17 May 2011; Accepted 26 May 2011

Academic Editor: Jun-Mo Yang

Copyright © 2011 Wei-Jiang Hu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract.

Creatine kinase (CK; EC 2.7.3.2) is related to several skin diseases such as psoriasis and dermatomyositis. CK is important in skin energy homeostasis because it catalyzes the reversible transfer of a phosphoryl group from MgATP to creatine. In this study, we predicted CK binding proteins via the use of bioinformatic tools such as protein-protein interaction (PPI) mappings and suggest the putative hub proteins for CK interactions. We obtained 123 proteins for brain type CK and 85 proteins for muscle type CK in the interaction networks. Among them, several hub proteins such as NFKB1, FHL2, MYOC, and ASB9 were predicted. Determination of the binding factors of CK can further promote our understanding of the roles of CK in physiological conditions.

1. Introduction

Creatine kinase (CK) (ATP: creatine kinase N-phosphotransferase, EC 2.7.3.2) is thought to be crucial for intracellular transport and the storage of high energy phosphate because it catalyzes the reversible transfer of a phosphoryl group from MgATP to creatine, which leads to the creation of phosphocreatine and MgADP [1]. CK plays an important role in the cellular energy metabolism of vertebrates, and it is widely distributed in tissues that require a lot of energy [2]. Several types of CK are expressed in various tissues: the muscle and brain types of CK are the most common, and three different isoenzymes that include CK-MM (the muscle type homodimer), CK-BB (the brain type homodimer), and CK-MB (the muscle plus brain type heterodimer) originate from these two common types. CK is an important serum marker for myocardial infarction. Various types of CKs (the muscle, brain, and mitochondrial types) are thought to be important not only in the diagnosis of myocardial infarction, cardiac hypertrophy, and muscular dystrophy but also for studies of some other serious diseases, including Alzheimer’s disease, Parkinson's disease, and psoriasis [3–8].

CK-BB is associated with several pathologies, including neurodegenerative and age-related diseases. Recently, Chang et al. [9] reported an important role for CK-BB in osteoclast-mediated bone resorption, which was found using a proteomics approach. They found that CK-BB is greatly increased during osteoclastogenesis and suggested that it represents a potential target for antiresorptive drug development. CK-BB interacts with the potassium-chloride cotransporter 3, which is involved in the pathophysiology of hereditary motor and sensory neuropathy with agenesis of the corpus callosum [10]. Previous studies [11, 12] have reported that CK-BB is involved in Alzheimer's disease (AD) as an oxidatively modified protein. This suggests that oxidatively damaged CK-BB may be associated with aging and age-related neurodegenerative disorders such as AD.

CK-MM is a good model to use for studying folding pathways because of several characteristics: (i) it is a dimer that consists of two identical subunits, each with an N-terminal domain with about 100 residues and a C-terminal domain with about 250 residues connected by a long linker [13]; (ii) extensively denatured CK can be renatured spontaneously with restoration of its enzymatic activity in the absence of any external assistance [14]; (iii) its folding pathway is complicated and involves several intermediates [15, 16]; (iv) conformational changes of the secondary and tertiary structures can be easily measured by monitoring activity changes [14, 15]; (v) protein-protein interactions, including molecular chaperones, are observed during refolding [17, 18].

In this study, we obtained computational predictions of the binding proteins by using two types of CK (CK-BB and CK-MM) as hub proteins in bioinformatic algorithms. As a result, we obtained 208 protein lists in the interaction networks via application of both muscle and brain types of CK. Determination of the binding factors and functions of CK can further promote our understanding of the physiological roles of CK.

2. Materials and Methods

2.1. PPI Mappings: PEIMAP and PSIMAP Algorithms

We present the functionally classified protein-protein interactions on the basis of the cell cycle, cell transport, oxidoreductase, and apoptosis. PPI resources were assembled from a combination of several experimental protein interaction databases. The protein interaction resources included six databases: DIP [19], BIND [20], IntAct [21], MINT [22], HPRD [23], and BioGrid [24]. We performed a redundancy test to remove identical protein sequences from the interaction databases. The databases contain 116,773 proteins and 229,799 interactions.

PPI prediction uses most of the major types of PPI algorithms. They are (1) Protein Structural Interactome MAP (PSIMAP), a method that uses the structural domain of the SCOP (Structural Classification of Proteins) database [25] and (2) Protein Experimental Interactome MAP (PEIMAP), a common method that uses public resources of experimental protein interaction information such as HPRD, BIND, DIP, MINT, IntAct; and BioGrid. The basic procedure of PSIMAP is to infer interactions between proteins by using their homologs. Interactions among domains or proteins for known PDB (Protein Data Bank) structures are the basis for the prediction. If an unknown protein has a homolog to a domain, then PSIMAP assumes that the query has the probability to interact with its homolog’s partners. This concept is called “homologous interaction.” The original interaction between two proteins or domains is based on the Euclidean distance. Therefore, PSIMAP gives a structure-based interaction prediction [26]. PEIMAP was constructed by combining several experimental protein-protein interaction databases. We carried out a redundancy check to remove identical protein sequences from the source interaction databases. The image was made by the Pajak2.00 program (http://vlado.fmf.uni-lj.si/pub/networks/pajek/).

3. Results and Discussion

We identified potential candidates through protein-protein interaction predictions made using various protein interaction resources. By analyzing the hub protein of the networks with metrics such as degree and centrality, we detected 123 potential candidates for CKB interacting (direct or indirect) factors and 85 candidates for CKM.

In Figure 1, interacting factors such as NFKB1 (NP_003989, nuclear factor of kappa light polypeptide gene enhancer in B-cells 1), MYOC (NP_000252; myocilin, trabecular meshwork inducible glucocorticoid response), MYOM2 (NP_003961; myomesin (M-protein) 2, 165 kDa), FHL2 (NP_001034581, four-and-a-half LIM domains 2), HIF1AN (NP_060372, hypoxia-inducible factor 1, alpha subunit inhibitor), ASB9 (NP_076992, ankyrin repeat and SOCS box-containing 9), and CKM (NP_001815, creatine kinase, muscle) were elucidated. Interestingly, NFKB1 was detected as a hub protein interacting with CK-BB in our results. In Figure 2, we obtained results similar to those from Figure 1, where NFKB1, MYOC, MYOM2, FHL2, HIF1AN, ASB9, and CKM were detected as interacting factors that were directly or indirectly associated with CKB. NFKB1, CKM, and ASB9 interacted with CKB directly.

Figure 1: PPI map for CKB as a target hub protein with the 80% identity. Labels with red color indicate the hub protein of targeting. The image was made by the aiSee program (http://www.aisee.com/).

Figure 2: PPI map for CKB as a target hub protein with the 100% identity. The methodological conditions were the same as for Figure 1 except the identity.

In the same way, we detected the CKM-associated proteins as shown in Figure 3 with 80% sequence identity. As a result, we found that CKB, FHL2, MYOC, ASB9, HIF1AN, NFKB1, TTN (NP_596870, titin), MYH9 (NP_002464, myosin, heavy chain 9, non-muscle), and ITGA7 (NP_002197, integrin, alpha 7) mainly interacted with CKM at 80% sequence identity. At the level of 100% identity, we found that MYOM2, CKB, FHL2, and MYOC directly interacted with CKM as shown in Figure 4. In addition to these factors, complete lists of factors that interacted with CKB and CKM in a direct or indirect manner are shown in Tables 1 and 2. After overlapping the results from Figures 1 to 4, we found that NFKB1, FHL2, and MYOC were still detected as hub proteins in Figure 5.

Table 1: Gene lists for the analyses of the PEIMAP and PSIMAP using CK-BB as a hub protein with 100% identity.

Gene ID
Gene symbol
Full name

6256
RXRA
Retinoid X receptor, alpha

3309
HSPA5
Heat shock 70 kDa protein 5 (glucose-regulated protein, 78 kDa)

3320
HSP90AA1
Heat shock protein 90 kDa alpha (cytosolic), class A member 1

2908
NR3C1
Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)

6778
STAT6
Signal transducer and activator of transcription 6, interleukin-4 induced

3146
HMGB1
High-mobility group box 1

3301
DNAJA1
DnaJ (Hsp40) homolog, subfamily A, member 1

4221
MEN1
Multiple endocrine neoplasia I

3312
HSPA8
Heat shock 70 kDa protein 8

3840
KPNA4
Karyopherin alpha 4 (importin alpha 3)

2274
FHL2
Four-and-a-half LIM domains 2

4792
NFKBIA
Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha

57805
KIAA1967
KIAA1967

3185
HNRNPF
Heterogeneous nuclear ribonucleoprotein F

203068
TUBB
Tubulin, beta

6774
STAT3
Signal transducer and activator of transcription 3 (acute-phase response factor)

4670
HNRNPM
Heterogeneous nuclear ribonucleoprotein M

1997
ELF1
E74-like factor 1 (ets domain transcription factor)

113457
TUBA3D
Tubulin, alpha 3D

1999
ELF3
E74-like factor 3 (ets domain transcription factor, epithelial-specific)

5591
PRKDC
Protein kinase, DNA-activated, catalytic polypeptide

708
C1QBP
Complement component 1, q subcomponent binding protein

2274
FHL2
Four-and-a-half LIM domains 2

3313
HSPA9
Heat shock 70 kDa protein 9 (mortalin)

8600
TNFSF11
Tumor necrosis factor (ligand) superfamily, member 11

3659
IRF1
Interferon regulatory factor 1

84617
TUBB6
Tubulin, beta 6

7280
TUBB2A
Tubulin, beta 2A

2908
NR3C1
Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)

2908
NR3C1
Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)

8517
IKBKG
Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma

7295
TXN
Thioredoxin

10318
TNIP1
TNFAIP3 interacting protein 1

4793
NFKBIB
Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta

3065
HDAC1
Histone deacetylase 1

3551
IKBKB
inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta

1152
CKB
Creatine kinase, brain

4069
LYZ
Lysozyme (renal amyloidosis)

140462
ASB9
Ankyrin repeat and SOCS box-containing 9

4653
MYOC
Myocilin, trabecular meshwork inducible glucocorticoid response

6774
STAT3
Signal transducer and activator of transcription 3 (acute-phase response factor)

3660
IRF2
Interferon regulatory factor 2

7278
TUBA3C
Tubulin, alpha 3c

4221
MEN1
Multiple endocrine neoplasia I

5966
REL
v-rel reticuloendotheliosis viral oncogene homolog (avian)

1147
CHUK
Conserved helix-loop-helix ubiquitous kinase

55922
NKRF
NFKB repressing factor

2113
ETS1
v-ets erythroblastosis virus E26 oncogene homolog 1 (avian)

64332
NFKBIZ
Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta

51773
RSF1
Remodeling and spacing factor 1

5971
RELB
v-rel reticuloendotheliosis viral oncogene homolog B

1832
DSP
Desmoplakin

347733
TUBB2B
Tubulin, beta 2B

2353
FOS
v-fos FBJ murine osteosarcoma viral oncogene homolog

9325
TRIP4
Thyroid hormone receptor interactor 4

4435
CITED1
Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1

22984
PDCD11
Programmed cell death 11

790
CAD
Carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase

1326
MAP3K8
Mitogen-activated protein kinase kinase kinase 8

1917
EEF1A2
Eukaryotic translation elongation factor 1 alpha 2

9172
MYOM2
Myomesin (M-protein) 2, 165 kDa

10856
RUVBL2
RuvB-like 2 (E. coli)

1158
CKM
Creatine kinase, muscle

808
CALM3
Calmodulin 3 (phosphorylase kinase, delta)

672
BRCA1
Breast cancer 1, early onset

801
CALM1
Calmodulin 1 (phosphorylase kinase, delta)

293
SLC25A6
Solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6

3310
HSPA6
Heat shock 70 kDa protein 6 (HSP70B′)

2908
NR3C1
Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)

136319
MTPN
Myotrophin

2274
FHL2
Four-and-a-half LIM domains 2

9093
DNAJA3
DnaJ (Hsp40) homolog, subfamily A, member 3

4628
MYH10
Myosin, heavy chain 10, non-muscle

4221
MEN1
Multiple endocrine neoplasia I

6774
STAT3
Signal transducer and activator of transcription 3 (acute-phase response factor)

3839
KPNA3
Karyopherin alpha 3 (importin alpha 4)

57805
KIAA1967
KIAA1967

2908
NR3C1
Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)

1869
E2F1
E2F transcription factor 1

55662
HIF1AN
Hypoxia-inducible factor 1, alpha subunit inhibitor

79155
TNIP2
TNFAIP3 interacting protein 2

9532
BAG2
BCL2-associated athanogene 2

6421
SFPQ
Splicing factor proline/glutamine-rich (polypyrimidine tract binding protein associated)

2908
NR3C1
Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)

10627
MRCL3
Myosin regulatory light chain MRCL3

7431
VIM
Vimentin

672
BRCA1
Breast cancer 1, early onset

2274
FHL2
Four-and-a-half LIM domains 2

4221
MEN1
Multiple endocrine neoplasia I

672
BRCA1
Breast cancer 1, early onset

4221
MEN1
Multiple endocrine neoplasia I

3836
KPNA1
Karyopherin alpha 1 (importin alpha 5)

3093
UBE2K
Ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)

805
CALM2
Calmodulin 2 (phosphorylase kinase, delta)

5970
RELA
v-rel reticuloendotheliosis viral oncogene homolog A (avian)

9782
MATR3
Matrin 3

8600
TNFSF11
Tumor necrosis factor (ligand) superfamily, member 11

8607
RUVBL1
RuvB-like 1 (E. coli)

4627
MYH9
Myosin, heavy chain 9, nonmuscle

23421
ITGB3BP
Integrin beta 3 binding protein (beta3-endonexin)

140462
ASB9
Ankyrin repeat and SOCS box-containing 9

4841
NONO
Non-POU domain containing, octamer-binding

9276
COPB2
Coatomer protein complex, subunit beta 2 (beta prime)

4221
MEN1
Multiple endocrine neoplasia I

1213
CLTC
Clathrin, heavy chain (Hc)

292
SLC25A5
Solute carrier family 25 (Mitochondrial carrier; adenine nucleotide translocator), member 5

4066
LYL1
Lymphoblastic leukemia-derived sequence 1

64332
NFKBIZ
Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta

5531
PPP4C
Protein phosphatase 4 (formerly X), catalytic subunit

8091
HMGA2
High-mobility group AT-hook 2

6202
RPS8
Ribosomal protein S8

1051
CEBPB
CCAAT/enhancer binding protein (C/EBP), beta

222643
UNC5CL
Unc-5 homolog C (C. elegans)-like

4790
NFKB1
Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1

71
ACTG1
Actin, gamma 1

3312
HSPA8
Heat shock 70 kDa protein 8

9782
MATR3
Matrin 3

3320
HSP90AA1
Heat shock protein 90 kDa alpha (cytosolic), class A member 1

4637
MYL6
Myosin, light chain 6, alkali, smooth muscle and nonmuscle

2908
NR3C1
Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)

4793
NFKBIB
Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta

688
KLF5
Kruppel-like factor 5 (intestinal)

672
BRCA1
Breast cancer 1, early onset

Table 2: Gene lists for the analyses of the PEIMAP and PSIMAP using CK-MM as a hub protein with 100% identity.

Gene ID
Gene symbol
Full name

1889
ECE1
Endothelin-converting enzyme 1

5981
RFC1
Replication factor C (activator 1) 1, 145 kDa

226
ALDOA
Aldolase A, fructose-bisphosphate

2335
FN1
Fibronectin 1

9372
ZFYVE9
Zinc finger, FYVE domain containing 9

60
ACTB
Actin, beta

3688
ITGB1
Integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)

7273
TTN
Titin

2274
FHL2
Four-and-a-half LIM domains 2

4853
NOTCH2
Notch homolog 2 (Drosophila)

2512
FTL
Ferritin, light polypeptide

1192
CLIC1
Chloride intracellular channel 1

2274
FHL2
Four-and-a-half LIM domains 2

5313
PKLR
Pyruvate kinase, liver and RBC

302
ANXA2
Annexin A2

7704
ZBTB16
Zinc finger and BTB domain containing 16

2200
FBN1
Fibrillin 1

27332
ZNF638
Zinc finger protein 638

92086
GGTLC1
Gamma-glutamyltransferase light chain 1

713
C1QB
Complement component 1, q subcomponent, B chain

3029
HAGH
Hydroxyacylglutathione hydrolase

5664
PSEN2
Presenilin 2 (Alzheimer disease 4)

7086
TKT
Transketolase (Wernicke-Korsakoff syndrome)

4176
MCM7
Minichromosome maintenance complex component 7

1152
CKB
Creatine kinase, brain

1499
CTNNB1
Catenin (cadherin-associated protein), beta 1, 88 kDa

140462
ASB9
Ankyrin repeat and SOCS box-containing 9

9457
FHL5
Four-and-a-half LIM domains 5

4653
MYOC
Myocilin, trabecular meshwork inducible glucocorticoid response

3029
HAGH
Hydroxyacylglutathione hydrolase

7704
ZBTB16
Zinc finger and BTB domain containing 16

3675
ITGA3
Integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)

226
ALDOA
Aldolase A, fructose-bisphosphate

3689
ITGB2
Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)

3688
ITGB1
Integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)

302
ANXA2
Annexin A2

92086
GGTLC1
Gamma-glutamyltransferase light chain 1

3679
ITGA7
Integrin, alpha 7

2023
ENO1
Enolase 1, (alpha)

9172
MYOM2
Myomesin (M-protein) 2, 165 kDa

1158
CKM
Creatine kinase, muscle

4790
NFKB1
Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105)

2
A2M
Alpha-2-macroglobulin

3688
ITGB1
Integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)

56944
OLFML3
Olfactomedin-like 3

1281
COL3A1
Collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)

2274
FHL2
Four-and-a-half LIM domains 2

3688
ITGB1
Integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)

118427
OLFM3
Olfactomedin 3

22900
CARD8
Caspase recruitment domain family, member 8

3488
IGFBP5
Insulin-like growth factor binding protein 5

7132
TNFRSF1A
Tumor necrosis factor receptor superfamily, member 1A

226
ALDOA
Aldolase A, fructose-bisphosphate

3675
ITGA3
Integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)

51455
REV1
REV1 homolog (S. cerevisiae)

6421
SFPQ
Splicing factor proline/glutamine-rich (polypyrimidine tract binding protein associated)

302
ANXA2
Annexin A2

4633
MYL2
Myosin, light chain 2, regulatory, cardiac, slow

8880
FUBP1
Far upstream element (FUSE) binding protein 1

2274
FHL2
Four-and-a-half LIM domains 2

3688
ITGB1
Integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)

27332
ZNF638
Zinc finger protein 638

3673
ITGA2
Integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)

203
AK1
Adenylate kinase 1

4627
MYH9
Myosin, heavy chain 9, non-muscle

5213
PFKM
Phosphofructokinase, muscle

140462
ASB9
Ankyrin repeat and SOCS box-containing 9

7076
TIMP1
TIMP metallopeptidase inhibitor 1

5176
SERPINF1
Serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1

3694
ITGB6
Integrin, beta 6

59
ACTA2
Actin, alpha 2, smooth muscle, aorta

4176
MCM7
Minichromosome maintenance complex component 7

10487
CAP1
CAP, adenylate cyclase-associated protein 1 (yeast)

7046
TGFBR1
Transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53 kDa)

3543
IGLL1
Immunoglobulin lambda-like polypeptide 1

5313
PKLR
Pyruvate kinase, liver and RBC

51455
REV1
REV1 homolog (S. cerevisiae)

10296
MAEA
Macrophage erythroblast attacher

3911
LAMA5
Laminin, alpha 5

2597
GAPDH
Glyceraldehyde-3-phosphate dehydrogenase

975
CD81
CD81 molecule

92086
GGTLC1
Gamma-glutamyltransferase light chain 1

1915
EEF1A1
Eukaryotic translation elongation factor 1 alpha 1

5664
PSEN2
Presenilin 2 (Alzheimer disease 4)

1278
COL1A2
Collagen, type I, alpha 2

Figure 3: PPI map for CKM as a target hub protein with the 80% identity. Labels with red color indicate the hub protein of targeting. The image was made by the aiSee program (http://www.aisee.com/).

Figure 4: PPI map for CKM as a target hub protein with the 100% identity. The methodological conditions were the same as for Figure 3 except the identity.

Figure 5: Overlapping map between CKB and CKM PPI maps. Data were input by using the results from Figures 1 to 4.

NFKB1 (also known as p50 or NF-kappaB) is a well-known transcription regulator that is responsible for the expression and regulation of many genes for immune response, cell adhesion, differentiation, proliferation, angiogenesis, and apoptosis [27–31]. It translocates into the nucleus and stimulates the expression of many genes involved in various biological functions. NFKB1 is also associated with a number of inflammatory diseases such as lymphoma [32], Alzheimer disease [33], psoriatic arthritis [34], breast cancer [35, 36], and rheumatoid arthritis [37]. Activation of NFKB1 requires binding of NF-kappaB essential modulator (NEMO) to ubiquitinated substrates [38]. With respect to an association with CK, it has been reported that NFKB1 is mostly associated with myocardial ischemia/reperfusion. During reperfusion, the absence of poly(ADP-ribose) polymerase-1 (PARP-1) leads to a reduction of myocardial apoptosis, which is associated with reduced NFKB1 activation [39, 40], and proteasome inhibition ablates activation of NFKB1 in myocardial reperfusion and reduces reperfusion injury [41]. Myocardial injury was assessed by measuring the serum levels of CK, and CK was reduced in serum along with reduction of NFKB1 activation.

FHL2 is a member of the human four-and-a-half-LIM-only protein family, which consists of the members FHL1, FHL2, FHL3, FHL4, and ACT. These proteins function in various cellular processes, including regulation of cell survival, transcription, and signal transduction [42]. FHL2 contains an LIM domain, one of the protein-protein interaction motifs, which allows specific proteins to combine with certain partners. The specificity of a protein-protein interaction can be obtained by an interaction code predicted by conserved amino acid sequences. The interaction of FHL2 with transcription factors and other proteins involved in cancer development was examined. Since transcription factors control all fundamental developmental and homeostatic processes, transcriptional cofactors such as FHL2 are likely to contribute to human carcinogenesis and are of clinical importance in various forms of cancer [43], including leukemia [44]. With respect to an association with CK, Chung et al. [45] reported that FHL2 (developmentally enhanced phosphotransfer enzyme-anchoring protein) amalgamated the myofibrillar CK metabolic signaling circuit, providing an energetic continuum between mitochondria and the nascent contractile machinery in a murine embryonic stem cell cardiac differentiation model. They reported that CK-M clustered around developing myofibrils, sarcolemma, and the perinuclear compartment, whereas CK-B was tightly associated with myofibrillar alpha-actinin, forming wire-like structures extending from the nuclear compartment to the sarcolemma. FHL2 was also increased in myocardial ischemia-reperfusion injury, where IL-6 and IL-8 mRNA are upregulated in human cardiac myocytes [46].

Recently, ASB9 was found to interact with ubiquitous mitochondrial CK [47]. The ankyrin repeat domains of ASB9 can associate with the substrate binding site of CK in a SOCS box-independent manner. The overexpression of ASB9 induces ubiquitination of CK. ASB9 reduces CK activities and cell growth and negatively regulates cell growth. ASB9 is a member of the ankyrin repeat and is a suppressor of the cytokine signaling (SOCS) box protein family. It can interact with the SOCS box domain of the elongin B-C adapter complex and can further complex with the cullin and ring box proteins to form E3 ubiquitin ligase complexes [48]. These complexes may be involved in specific substrate-recognition for ubiquitination and degradation and mediate the substrate-recognition of the E3 ubiquitin ligases.

The interaction between CK and MYOC has not been elucidated. However, MYOC has a cytoskeletal function, and this implies that it may interact with CK somehow. MYOC is expressed in many ocular tissues including the trabecular meshwork [49], which is a specialized eye tissue that is essential in regulating intraocular pressure. MYOC mutations have been identified as the cause of hereditary juvenile-onset open-angle glaucoma [50].

Researchers could apply computational prediction by PPI mapping to help determine target proteins. Since the next step in the functional study of interesting proteins/genes is a time- and cost-consuming process, the number of target proteins is limited; hence, for the right choice, computational prediction on the basis of database information could be critical at this step. Functional studies can be further conducted using a mouse model and a large number of clinical samples. Final confirmation and CK mechanisms could then be more clearly evaluated for developing drugs to effectively treat CK-related diseases.

The functions of most of the candidate proteins predicted in this study have not been well reported in skin diseases or in the pathogenesis of other diseases. We provide new information regarding these candidate proteins’ interaction with CK, as well as the involvement of several hub proteins such as NFKB1, FHL2, ASB9, and MYOC. Although we do not suggest a direct role of any candidate protein in skin diseases, we provide candidate proteins to be targeted in further studies of CK-associated diagnostic markers and/or treatment of corresponding skin conditions. Furthermore, we also provide some insights into understanding the responses of CK in skin.

Abbreviations

PPI: | Protein-protein interaction
CK-MM: | Muscle type homodimer
CK-BB: | Brain type homodimer.

Acknowledgments

This study was supported by the Grants from the Science and Technology Bureau of Jiaxing, Zhejiang (no. 2008AY2032) and the Science and Technology Planning Project of Zhejiang Province (no. 2010C33139). Dr. W.-J. Hu was supported by a Grant from China Postdoctoral Science Foundation (no. 20060400467). Dr. S.-M. Zhou was supported by a grant from the Science and Technology Bureau of Jiaxing (no. 2007AY2021).

References

U. Schlattner, M. Forstner, M. Eder, O. Stachowiak, K. Fritz-Wolf, and T. Wallimann, “Functional aspects of the X-ray structure of mitochondrial creatine kinase: a molecular physiology approach,” Molecular and Cellular Biochemistry, vol. 184, no. 1-2, pp. 125–140, 1998.

M. J. McLeish and G. L. Kenyon, “Relating structure to mechanism in creatine kinase,” Critical Reviews in Biochemistry and Molecular Biology, vol. 40, no. 1, pp. 1–20, 2005.

D. R. Abendschein, “Rapid diagnosis of myocardial infarction and reperfusion by assay of plasma isoforms of creatine kinase isoenzymes,” Clinical Biochemistry, vol. 23, no. 5, pp. 399–407, 1990.

S. H. Smith, M. F. Kramer, I. Reis, S. P. Bishop, and J. S. Ingwall, “Regional changes in creatine kinase and myocyte size in hypertensive and nonhypertensive cardiac hypertrophy,” Circulation Research, vol. 67, no. 6, pp. 1334–1344, 1990.

E. Ozawa, Y. Hagiwara, and M. Yoshida, “Creatine kinase, cell membrane and Duchenne muscular dystrophy,” Molecular and Cellular Biochemistry, vol. 190, no. 1-2, pp. 143–151, 1999.

T. S. Bürklen, U. Schlattner, R. Homayouni et al., “The creatine kinase/creatine connection to alzheimer's disease: CK-inactivation, APP-CK complexes and focal creatine deposits,” Journal of Biomedicine and Biotechnology, vol. 2006, no. 3, Article ID 35936, 11 pages, 2006.

H. Takubo, S. Shimoda-Matsubayashi, and Y. Mizuno, “Serum creatine kinase is elevated in patients with Parkinson's disease: a case controlled study,” Parkinsonism and Related Disorders, vol. 9, supplement 1, pp. S43–S46, 2003.

U. Schlattner, N. Möckli, O. Speer, S. Werner, and T. Wallimann, “Creatine kinase and creatine transporter in normal, wounded, and diseased skin,” Journal of Investigative Dermatology, vol. 118, no. 3, pp. 416–423, 2002.

E. J. Chang, J. Ha, F. Oerlemans et al., “Brain-type creatine kinase has a crucial role in osteoclast-mediated bone resorption,” Nature Medicine, vol. 14, no. 9, pp. 966–972, 2008.

A. Salin-Cantegrel, M. Shekarabi, S. Holbert et al., “HMSN/ACC truncation mutations disrupt brain-type creatine kinase-dependant activation of K⁺/Cl- co-transporter 3,” Human Molecular Genetics, vol. 17, no. 17, pp. 2703–2711, 2008.

A. Castegna, M. Aksenov, M. Aksenova et al., “Proteomic identification of oxidatively modified proteins in Alzheimer's disease brain. Part I: creatine kinase BB, glutamine synthase, and ubiquitin carboxy-terminal hydrolase L-1,” Free Radical Biology and Medicine, vol. 33, no. 4, pp. 562–571, 2002.

M. Aksenov, M. Aksenova, D. A. Butterfield, and W. R. Markesbery, “Oxidative modification of creatine kinase BB in Alzheimer's disease brain,” Journal of Neurochemistry, vol. 74, no. 6, pp. 2520–2527, 2000.

J. K. Rao, G. Bujacz, and A. Wlodawer, “Crystal structure of rabbit muscle creatine kinase,” FEBS Letters, vol. 439, no. 1-2, pp. 133–137, 1998.

H. M. Zhou and C. L. Tsou, “Comparison of activity and conformation changes during refolding of urea-denatured creatine kinase,” Biochimica et Biophysica Acta, vol. 869, no. 1, pp. 69–74, 1986.

Y. D. Park, W. B. Ou, T. W. Yu, and H. M. Zhou, “Folding pathway for partially folded rabbit muscle creatine kinase,” Biochemistry and Cell Biology, vol. 79, no. 4, pp. 479–487, 2001.

Y. D. Park, Z. F. Cao, and H. M. Zhou, “Reactivation kinetics of guanidine hydrochloride-denatured creatine kinase measured using the substrate reaction,” Journal of Protein Chemistry, vol. 20, no. 1, pp. 67–72, 2001.

S. Li, J. H. Bai, Y. D. Park, and H. M. Zhou, “Capture of monomeric refolding intermediate of human muscle creatine kinase,” Protein Science, vol. 15, no. 1, pp. 171–181, 2006.

W. B. Ou, W. Luo, Y. D. Park, and H. M. Zhou, “Chaperone-like activity of peptidyl-prolyl cis-trans isomerase during creatine kinase refolding,” Protein Science, vol. 10, no. 11, pp. 2346–2353, 2001.

I. Xenarios, D. W. Rice, L. Salwinski, M. K. Baron, E. M. Marcotte, and D. Eisenberg, “DIP: the database of interacting proteins,” Nucleic Acids Research, vol. 28, no. 1, pp. 289–291, 2000.

G. D. Bader, I. Donaldson, C. Wolting, B. F. Ouellette, T. Pawson, and C. W. Hogue, “BIND—the biomolecular interaction network database,” Nucleic Acids Research, vol. 29, no. 1, pp. 242–245, 2001.

H. Hermjakob, L. Montecchi-Palazzi, C. Lewington et al., “IntAct: an open source molecular interaction database,” Nucleic Acids Research, vol. 32, pp. D452–D455, 2004.

A. Zanzoni, L. Montecchi-Palazzi, M. Quondam, G. Ausiello, M. Helmer-Citterich, and G. Cesareni, “MINT: a molecular INTeraction database,” FEBS Letters, vol. 513, no. 1, pp. 135–140, 2002.

S. Peri, J. D. Navarro, T. Z. Kristiansen et al., “Human protein reference database as a discovery resource for proteomics,” Nucleic Acids Research, vol. 32, pp. D497–D501, 2004.

C. Stark, B. J. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, and M. Tyers, “BioGRID: a general repository for interaction datasets,” Nucleic Acids Research, vol. 34, pp. D535–D539, 2006.

A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, “SCOP: a structural classification of proteins database for the investigation of sequences and structures,” Journal of Molecular Biology, vol. 247, no. 4, pp. 536–540, 1995.

J. Park, M. Lappe, and S. A. Teichmann, “Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast,” Journal of Molecular Biology, vol. 307, no. 3, pp. 929–938, 2001.

X. F. Sun and H. Zhang, “NFKB and NFKBI polymorphisms in relation to susceptibility of tumour and other diseases,” Histology and Histopathology, vol. 22, no. 12, pp. 1387–1398, 2007.

S. Patel and D. Santani, “Role of NF-κB in the pathogenesis of diabetes and its associated complications,” Pharmacological Reports, vol. 61, no. 4, pp. 595–603, 2009.

L. Verstrepen, I. Carpentier, K. Verhelst, and R. Beyaert, “ABINs: a 20 binding inhibitors of NF-κB and apoptosis signaling,” Biochemical Pharmacology, vol. 78, no. 2, pp. 105–114, 2009.

S. P. Tabruyn and A. W. Griffioen, “NF-κB: a new player in angiostatic therapy,” Angiogenesis, vol. 11, no. 1, pp. 101–106, 2008.

T. Okamoto, T. Sanda, and K. Asamitsu, “NK-κB signaling and carcinogenesis,” Current Pharmaceutical Design, vol. 13, no. 5, pp. 447–462, 2007.

Q. Qiao, Y. Nozaki, K. Sakoe, N. Komatsu, and K. Kirito, “NF-κB mediates aberrant activation of HIF-1 in malignant lymphoma,” Experimental Hematology, vol. 38, no. 12, pp. 1199–1208, 2010.

J. G. Cui, Y. Y. Li, Y. Zhao, S. Bhattacharjee, and W. J. Lukiw, “Differential regulation of interleukin-1 receptor-associated kinase-1 (IRAK-1) and IRAK-2 by microRNA-146a and NF-κB in stressed human astroglial cells and in Alzheimer disease,” Journal of Biological Chemistry, vol. 285, no. 50, pp. 38951–38960, 2010.

C. Butt, S. Sun, L. Peddle et al., “Association of nuclear factor-κB in psoriatic arthritis,” Journal of Rheumatology, vol. 32, no. 9, pp. 1742–1744, 2005.

S. J. van Laere, I. van der Auwera, G. G. van den Eynden et al., “Nuclear factor-κB signature of inflammatory breast cancer by cDNA microarray validated by quantitative real-time reverse transcription-PCR, immunohistochemistry, and nuclear factor-κB DNA-binding,” Clinical Cancer Research, vol. 12, no. 11, pp. 3249–3256, 2006.

F. Lerebours, S. Vacher, C. Andrieu et al., “NF-κ B genes have a major role in inflammatory breast cancer,” BMC Cancer, vol. 8, p. 41, 2008.

S. S. Makarov, “NF-κ B in rheumatoid arthritis: a pivotal regulator of inflammation, hyperplasia, and tissue destruction,” Arthritis Research, vol. 3, no. 4, pp. 200–206, 2001.

S. Rahighi, F. Ikeda, M. Kawasaki et al., “Specific recognition of linear ubiquitin chains by NEMO is important for NF-κB activation,” Cell, vol. 136, no. 6, pp. 1098–1109, 2009.

B. Zingarelli, P. W. Hake, M. O'Connor, A. Denenberg, S. Kong, and B. J. Aronow, “Absence of poly(ADP-ribose)polymerase-1 alters nuclear factor-κ B activation and gene expression of apoptosis regulators after reperfusion injury,” Molecular Medicine, vol. 9, no. 5–8, pp. 143–153, 2003.

J. Yang, J. J. Marden, C. Fan et al., “Genetic redox preconditioning differentially modulates AP-1 and NFκB responses following cardiac ischemia/reperfusion injury and protects against necrosis and apoptosis,” Molecular Therapy, vol. 7, no. 3, pp. 341–353, 2003.

J. Pye, F. Ardeshirpour, A. McCain et al., “Proteasome inhibition ablates activation of NF-κB in myocardial reperfusion and reduces reperfusion injury,” American Journal of Physiology, vol. 284, no. 3, pp. H919–H926, 2003.

M. Johannessen, S. Møler, T. Hansen, U. Moens, and M. van Ghelue, “The multifunctional roles of the four-and-a-half-LIM only protein FHL2,” Cellular and Molecular Life Sciences, vol. 63, no. 3, pp. 268–284, 2006.

K. Kleiber, K. Strebhardt, and B. T. Martin, “The biological relevance of FHL2 in tumour cells and its role as a putative cancer target,” Anticancer Research, vol. 27, no. 1 A, pp. 55–61, 2007.

Z. Qian, J. M. Joslin, T. R. Tennant et al., “Cytogenetic and genetic pathways in therapy-related acute myeloid leukemia,” Chemico Biological Interactions, vol. 184, no. 1-2, pp. 50–57, 2010.

S. Chung, P. P. Dzeja, R. S. Faustino, and A. Terzic, “Developmental restructuring of the creatine kinase system integrates mitochondrial energetics with stem cell cardiogenesis,” Annals of the New York Academy of Sciences, vol. 1147, pp. 254–263, 2008.

S. Wan, A. P. Yim, C. K. Wong et al., “Expression of FHL2 and cytokine messenger RNAs in human myocardium after cardiopulmonary bypass,” International Journal of Cardiology, vol. 86, no. 2-3, pp. 265–272, 2002.

S. Kwon, D. Kim, J. W. Rhee et al., “ASB9 interacts with ubiquitous mitochondrial creatine kinase and inhibits mitochondrial function,” BMC Biology, vol. 8, p. 23, 2010.

X. Fei, Y. Zhang, X. Gu, R. Qiu, Y. Mao, and C. Ji, “Crystallization and preliminary X-ray analysis of the splice variant of human ankyrin repeat and suppressor of cytokine signaling box protein 9 (hASB9-2),” Protein and Peptide Letters, vol. 16, no. 3, pp. 333–335, 2009.

M. K. Joe, S. Sohn, T. E. Kim, J. E. Im, Y. R. Choi, and C. Kee, “Analysis of glucocorticoid-induced MYOC expression in human trabecular meshwork cells,” Vision Research, vol. 51, no. 9, pp. 1033–1038, 2011.

X. Zhao, C. Yang, Y. Tong, X. Zhang, L. Xu, and Y. Li, “Identification a novel MYOC gene mutation in a Chinese family with juvenile-onset open angle glaucoma,” Molecular Vision, vol. 16, pp. 1728–1735, 2010.