A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System

PLoS Computational Biology - Tập 7 Số 1 - Trang e1001059
Bing Liu1,2, Jing Zhang3,1, Pei Yi Tan3, David Hsu2, Anna M. Blom4, Benjamin Sieu‐Hon Leong5, Sunil Sethi6, Bow Ho7, Jeak Ling Ding3,8, P. S. Thiagarajan2
1NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
2School of Computing, National University of Singapore, Singapore
3Department of Biological Sciences, National University of Singapore, National University of Singapore, Singapore
4Department of Laboratory Medicine, Lund University, Malmö, Sweden
5Emergency Medicine Department, National University Hospital, Singapore
6Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
7Department of Microbiology, Yong Loo Lin School of Medicine, Singapore
8Singapore-MIT Alliance, National University of Singapore,  , Singapore

Tóm tắt

Từ khóa


Tài liệu tham khảo

MJ Walport, 2001, Complement. First of two parts., N Engl J Med, 344, 1058

DT Fearon, 1998, The complement system and adaptive immunity., Semin Immunol, 10, 355, 10.1006/smim.1998.0137

DT Fearon, 1996, The instructive role of innate immunity in the acquired immune response., Science, 272, 50, 10.1126/science.272.5258.50

Z Fishelson, 2001, Complement and apoptosis., Mol Immunol, 38, 207, 10.1016/S0161-5890(01)00055-4

MJ Walport, 2001, Complement. Second of two parts., N Engl J Med, 344, 1140

M Okroj, 2007, Rheumatoid arthritis and the complement system., Ann Med, 39, 517, 10.1080/07853890701477546

L Truedsson, 2007, Complement deficiencies and systemic lupus erythematosus., Autoimmunity, 40, 560, 10.1080/08916930701510673

R Veerhuis, 2005, Amyloid associated proteins in Alzheimer's and prion disease., Curr Drug Targets CNS Neurol Disord, 4, 235, 10.2174/1568007054038184

DH Anderson, 2010, The pivotal role of the complement system in aging and age-related macular degeneration: hypothesis re-visited., Prog Retin Eye Res, 29, 95, 10.1016/j.preteyeres.2009.11.003

AP Sjoberg, 2009, Complement activation and inhibition: a delicate balance., Trends Immunol, 30, 83, 10.1016/j.it.2008.11.003

C Mold, 1981, C-reactive protein is protective against Streptococcus pneumoniae infection in mice., J Exp Med, 154, 1703, 10.1084/jem.154.5.1703

L Marnell, 2005, C-reactive protein: ligands, receptors and role in inflammation., Clin Immunol, 117, 104, 10.1016/j.clim.2005.08.004

T Fujita, 2004, The lectin-complement pathway–its role in innate immunity and evolution., Immunol Rev, 198, 185, 10.1111/j.0105-2896.2004.0123.x

PM Ng, 2007, C-reactive protein collaborates with plasma lectins to boost immune response against bacteria., EMBO J, 26, 3431, 10.1038/sj.emboj.7601762

J Zhang, 2009, Local inflammation induces complement crosstalk which amplifies the antimicrobial response., PLoS Pathog, 5, e1000282, 10.1371/journal.ppat.1000282

JH Griffin, 1992, Reevaluation of total, free, and bound protein S and C4b-binding protein levels in plasma anticoagulated with citrate or hirudin., Blood, 79, 3203, 10.1182/blood.V79.12.3203.bloodjournal79123203

SR Barnum, 1990, C4b-binding protein, a regulatory component of the classical pathway of complement, is an acute-phase protein and is elevated in systemic lupus erythematosus., Complement Inflamm, 7, 71, 10.1159/000463131

LM Boerger, 1987, Oral contraceptives and gender affect protein S status., Blood, 69, 692, 10.1182/blood.V69.2.692.692

AM Blom, 2001, Structural requirements for the complement regulatory activities of C4BP., J Biol Chem, 276, 27136, 10.1074/jbc.M102445200

AM Blom, 1999, A cluster of positively charged amino acids in the C4BP alpha-chain is crucial for C4b binding and factor I cofactor function., J Biol Chem, 274, 19237, 10.1074/jbc.274.27.19237

J Scharfstein, 1978, Human C4-binding protein. I. Isolation and characterization., J Exp Med, 148, 207, 10.1084/jem.148.1.207

I Gigli, 1979, Prosser White Oration 1978. The complement system in inflammation and host defence., Clin Exp Dermatol, 4, 271

AP Sjoberg, 2006, Regulation of complement activation by C-reactive protein: targeting of the inhibitory activity of C4b-binding protein., J Immunol, 176, 7612, 10.4049/jimmunol.176.12.7612

AM Blom, 2009, C4b-binding protein (C4BP) inhibits development of experimental arthritis in mice., Ann Rheum Dis, 68, 136, 10.1136/ard.2007.085753

B Liu, 2009, Probabilistic approximations of signaling pathway dynamics., 251

KP Murphy, 2002, Dynamic Bayesian Networks: Representation, inference and learning.

H Hirayama, 1996, Linear systems analysis of activating processes of complement system as a defense mechanism., Biosystems, 39, 173, 10.1016/0303-2647(96)01617-6

AA Korotaevskiy, 2009, Non-linear dynamics of the complement system activation., Math Biosci, 222, 127, 10.1016/j.mbs.2009.10.003

B Selander, 2006, Mannan-binding lectin activates C3 and the alternative complement pathway without involvement of C2., J Clin Invest, 116, 1425, 10.1172/JCI25982

MH Kaplan, 1974, Interaction of C-reactive protein complexes with the complement system. I. Consumption of human complement associated with the reaction of C-reactive protein with pneumococcal C-polysaccharide and with the choline phosphatides, lecithin and sphingomyelin., J Immunol, 112, 2135

MV Suresh, 2004, Interaction of calcium-bound C-reactive protein with fibronectin is controlled by pH: in vivo implications., J Biol Chem, 279, 52552, 10.1074/jbc.M409054200

D Ricklin, 2007, Complement-targeted therapeutics., Nat Biotechnol, 25, 1265, 10.1038/nbt1342

A Krarup, 2004, L-ficolin is a pattern recognition molecule specific for acetyl groups., J Biol Chem, 279, 47513, 10.1074/jbc.M407161200

M Matsushita, 2001, Activation of the lectin complement pathway by ficolins., Int Immunopharmacol, 1, 359, 10.1016/S1567-5769(00)00045-X

I Gigli, 1979, Modulation of the classical pathway C3 convertase by plasma proteins C4 binding protein and C3b inactivator., Proc Natl Acad Sci U S A, 76, 6596, 10.1073/pnas.76.12.6596

X Ji, 2006, libSRES: a C library for stochastic ranking evolution strategy for parameter estimation., Bioinformatics, 22, 124, 10.1093/bioinformatics/bti753

J Gunawardena, 2010, Models in systems biology: the parameter problem and the meanings of robustness., 21

NA van Riel, 2006, Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments., Brief Bioinform, 7, 364, 10.1093/bib/bbl040

S Hoops, 2006, COPASI–a COmplex PAthway SImulator., Bioinformatics, 22, 3067, 10.1093/bioinformatics/btl485

Z Zi, 2005, In silico identification of the key components and steps in IFN-gamma induced JAK-STAT signaling pathway., FEBS Lett, 579, 1101, 10.1016/j.febslet.2005.01.009

CJ Langmead, 2006, Temporal-logics as query languages for dynamic Bayesian networks: application to D. melanogaster embryo development.

S Jha, 2009, A Bayesian approach to model checking biological systems., 218

M Bozga, 1999, On the representation of probabilities over structured domains., 682

M Jaeger, 2004, Probabilistic decision graphs – combining verification and AI techniques for probabilistic inference., Int J Uncertain Fuzz, 12, 19, 10.1142/S0218488504002564

G Koh, 2010, Incremental signaling pathway modeling by data integration., 281

N Rawal, 2009, Stringent regulation of complement lectin pathway C3/C5 convertase by C4b-binding protein (C4BP)., Mol Immunol, 46, 2902, 10.1016/j.molimm.2009.07.006

V Kirjavainen, 2008, Yersinia enterocolitica serum resistance proteins YadA and ail bind the complement regulator C4b-binding protein., PLoS Pathog, 4, e1000140, 10.1371/journal.ppat.1000140

A Thern, 1995, Ig-binding surface proteins of Streptococcus pyogenes also bind human C4b-binding protein (C4BP), a regulatory component of the complement system., J Immunol, 154, 375, 10.4049/jimmunol.154.1.375

S Ram, 2001, Binding of C4b-binding protein to porin: a molecular mechanism of serum resistance of Neisseria gonorrhoeae., J Exp Med, 193, 281, 10.1084/jem.193.3.281

NV Prasadarao, 2002, A novel interaction of outer membrane protein A with C4b binding protein mediates serum resistance of Escherichia coli K1., J Immunol, 169, 6352, 10.4049/jimmunol.169.11.6352

T Nordstrom, 2004, The emerging pathogen Moraxella catarrhalis interacts with complement inhibitor C4b binding protein through ubiquitous surface proteins A1 and A2., J Immunol, 173, 4598, 10.4049/jimmunol.173.7.4598

T Meri, 2004, The hyphal and yeast forms of Candida albicans bind the complement regulator C4b-binding protein., Infect Immun, 72, 6633, 10.1128/IAI.72.11.6633-6641.2004

K Berggard, 1997, Bordetella pertussis binds the human complement regulator C4BP: role of filamentous hemagglutinin., Infect Immun, 65, 3638, 10.1128/IAI.65.9.3638-3643.1997

KP Murphy, 2001, The factored frontier algorithm for approximate inference in DBNs., 378

D Sheskin, 2004, Handbook of parametric and nonparametric statistical procedures, 10.4324/9780203489536

AF Zadura, 2009, Complement inhibitor C4b-binding protein in primary Sjogren's syndrome and its association with other disease markers., Scand J Immunol, 69, 374, 10.1111/j.1365-3083.2009.02229.x

B Dahlback, 1983, Purification of human C4b-binding protein and formation of its complex with vitamin K-dependent protein S., Biochem J, 209, 847, 10.1042/bj2090847