메뉴 건너뛰기




Volumn 80, Issue 12, 2012, Pages 2666-2679

Predicting Ca 2+-binding sites using refined carbon clusters

Author keywords

Ca 2+ binding proteins; Carbon clusters; Graph theory; NMR; Side chain center of mass

Indexed keywords

BINDING PROTEIN; CALCIUM; CARBON; LEAD; LIGAND; MAGNESIUM; OXYGEN; ZINC; CALCIUM BINDING PROTEIN; CALMODULIN; CELL CYCLE PROTEIN; CETN2 PROTEIN, HUMAN;

EID: 84868192107     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24149     Document Type: Article
Times cited : (15)

References (63)
  • 1
    • 0036182380 scopus 로고    scopus 로고
    • Calcium and oxidative stress: from cell signaling to cell death
    • Ermak G, Davies KJ. Calcium and oxidative stress: from cell signaling to cell death. Mol Immunol 2002; 38: 713-721.
    • (2002) Mol Immunol , vol.38 , pp. 713-721
    • Ermak, G.1    Davies, K.J.2
  • 2
    • 0032531818 scopus 로고    scopus 로고
    • Calcium-a life and death signal
    • Berridge MJ, Bootman MD, Lipp P. Calcium-a life and death signal. Nature 1998; 395: 645-648.
    • (1998) Nature , vol.395 , pp. 645-648
    • Berridge, M.J.1    Bootman, M.D.2    Lipp, P.3
  • 4
    • 33750046332 scopus 로고    scopus 로고
    • Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins
    • Zhou Y, Yang W, Kirberger M, Lee HW, Ayalasomayajula G, Yang JJ. Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins. Proteins 2006; 65: 643-655.
    • (2006) Proteins , vol.65 , pp. 643-655
    • Zhou, Y.1    Yang, W.2    Kirberger, M.3    Lee, H.W.4    Ayalasomayajula, G.5    Yang, J.J.6
  • 5
    • 0029671219 scopus 로고    scopus 로고
    • 2+-binding protein ALG-2 and Alzheimer's disease gene ALG-3
    • 2+-binding protein ALG-2 and Alzheimer's disease gene ALG-3. Science 1996; 271: 521-525.
    • (1996) Science , vol.271 , pp. 521-525
    • Vito, P.1    Lacana, E.2    D'Adamio, L.3
  • 8
    • 0016346438 scopus 로고
    • Calcium and potassium disturbances in acute leukemia
    • Hocker P, Reizenstein P. Calcium and potassium disturbances in acute leukemia. Blut 1974; 29: 398-406.
    • (1974) Blut , vol.29 , pp. 398-406
    • Hocker, P.1    Reizenstein, P.2
  • 10
    • 54049137686 scopus 로고    scopus 로고
    • Switching of G-protein usage by the calcium-sensing receptor reverses its effect on parathyroid hormone-related protein secretion in normal versus malignant breast cells
    • Mamillapalli R, VanHouten J, Zawalich W, Wysolmerski J. Switching of G-protein usage by the calcium-sensing receptor reverses its effect on parathyroid hormone-related protein secretion in normal versus malignant breast cells. J Biol Chem 2008; 283: 24435-24447.
    • (2008) J Biol Chem , vol.283 , pp. 24435-24447
    • Mamillapalli, R.1    VanHouten, J.2    Zawalich, W.3    Wysolmerski, J.4
  • 11
    • 63649143578 scopus 로고    scopus 로고
    • Melittin, a major component of bee venom, sensitizes human hepatocellular carcinoma cells to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis by activating CaMKII-TAK1-JNK/p38 and inhibiting IκBα kinase-NFκB
    • Wang C, Chen T, Zhang N, Yang M, Li B, Lu X, Cao X, Ling C. Melittin, a major component of bee venom, sensitizes human hepatocellular carcinoma cells to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis by activating CaMKII-TAK1-JNK/p38 and inhibiting IκBα kinase-NFκB. J Biol Chem 2009; 284: 3804-3813.
    • (2009) J Biol Chem , vol.284 , pp. 3804-3813
    • Wang, C.1    Chen, T.2    Zhang, N.3    Yang, M.4    Li, B.5    Lu, X.6    Cao, X.7    Ling, C.8
  • 12
    • 54049150008 scopus 로고    scopus 로고
    • Calpain-mediated androgen receptor breakdown in apoptotic prostate cancer cells
    • Yang H, Murthy S, Sarkar FH, Sheng S, Reddy GP, Dou QP. Calpain-mediated androgen receptor breakdown in apoptotic prostate cancer cells. J Cell Physiol 2008; 217: 569-576.
    • (2008) J Cell Physiol , vol.217 , pp. 569-576
    • Yang, H.1    Murthy, S.2    Sarkar, F.H.3    Sheng, S.4    Reddy, G.P.5    Dou, Q.P.6
  • 14
    • 0034711229 scopus 로고    scopus 로고
    • Crystal structures of apo- and holo-bovine α-lactalbumin at 2.2-Å resolution reveal an effect of calcium on inter-lobe interactions
    • Chrysina ED, Brew K, Acharya KR. Crystal structures of apo- and holo-bovine α-lactalbumin at 2.2-Å resolution reveal an effect of calcium on inter-lobe interactions. J Biol Chem 2000; 275: 37021-37029.
    • (2000) J Biol Chem , vol.275 , pp. 37021-37029
    • Chrysina, E.D.1    Brew, K.2    Acharya, K.R.3
  • 16
    • 0026410002 scopus 로고
    • Structural aspects of metal liganding to functional groups in proteins
    • Glusker JP. Structural aspects of metal liganding to functional groups in proteins. Adv Protein Chem 1991; 42: 1-76.
    • (1991) Adv Protein Chem , vol.42 , pp. 1-76
    • Glusker, J.P.1
  • 17
    • 0034856791 scopus 로고    scopus 로고
    • Structural characteristics of protein binding sites for calcium and lanthanide ions
    • Pidcock E, Moore GR. Structural characteristics of protein binding sites for calcium and lanthanide ions. J Biol Inorg Chem 2001; 6: 479-489.
    • (2001) J Biol Inorg Chem , vol.6 , pp. 479-489
    • Pidcock, E.1    Moore, G.R.2
  • 19
    • 35348992596 scopus 로고    scopus 로고
    • The N1317H substitution associated with Leber congenital amaurosis results in impaired interdomain packing in human CRB1 epidermal growth factor-like (EGF) domains
    • Davis JA, Handford PA, Redfield C. The N1317H substitution associated with Leber congenital amaurosis results in impaired interdomain packing in human CRB1 epidermal growth factor-like (EGF) domains. J Biol Chem 2007; 282: 28807-28814.
    • (2007) J Biol Chem , vol.282 , pp. 28807-28814
    • Davis, J.A.1    Handford, P.A.2    Redfield, C.3
  • 21
    • 0026409654 scopus 로고
    • Calcium-binding sites in proteins: a structural perspective
    • McPhalen CA, Strynadka NC, James MN. Calcium-binding sites in proteins: a structural perspective. Adv Protein Chem 1991; 42: 77-144.
    • (1991) Adv Protein Chem , vol.42 , pp. 77-144
    • McPhalen, C.A.1    Strynadka, N.C.2    James, M.N.3
  • 22
    • 0023471689 scopus 로고
    • Calcium coordination and the calmodulin fold: divergent versus convergent evolution
    • Kretsinger RH. Calcium coordination and the calmodulin fold: divergent versus convergent evolution. Cold Spring Harb Symp Quant Biol 1987; 52: 499-510.
    • (1987) Cold Spring Harb Symp Quant Biol , vol.52 , pp. 499-510
    • Kretsinger, R.H.1
  • 24
    • 0242500908 scopus 로고    scopus 로고
    • First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations
    • Dudev T, Lin YL, Dudev M, Lim C. First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations. J Am Chem Soc 2003; 125: 3168-3180.
    • (2003) J Am Chem Soc , vol.125 , pp. 3168-3180
    • Dudev, T.1    Lin, Y.L.2    Dudev, M.3    Lim, C.4
  • 25
    • 40549094379 scopus 로고    scopus 로고
    • Combining molecular dynamics and machine learning to improve protein function recognition
    • Glazer DS, Radmer RJ, Altman RB. Combining molecular dynamics and machine learning to improve protein function recognition. Pac Symp Biocomput 2008; 13: 332-343.
    • (2008) Pac Symp Biocomput , vol.13 , pp. 332-343
    • Glazer, D.S.1    Radmer, R.J.2    Altman, R.B.3
  • 26
    • 57249116902 scopus 로고    scopus 로고
    • Predicting small ligand binding sites in proteins using backbone structure
    • Bordner AJ. Predicting small ligand binding sites in proteins using backbone structure. Bioinformatics 2008; 24: 2865-2871.
    • (2008) Bioinformatics , vol.24 , pp. 2865-2871
    • Bordner, A.J.1
  • 31
    • 33744803962 scopus 로고    scopus 로고
    • Predicting calcium-binding sites in proteins-a graph theory and geometry approach
    • Deng H, Chen G, Yang W, Yang JJ. Predicting calcium-binding sites in proteins-a graph theory and geometry approach. Proteins 2006; 64: 34-42.
    • (2006) Proteins , vol.64 , pp. 34-42
    • Deng, H.1    Chen, G.2    Yang, W.3    Yang, J.J.4
  • 32
    • 66149162969 scopus 로고    scopus 로고
    • 2+-binding sites with different coordination numbers in proteins with atomic resolution
    • 2+-binding sites with different coordination numbers in proteins with atomic resolution. Proteins 2009; 75: 787-798.
    • (2009) Proteins , vol.75 , pp. 787-798
    • Wang, X.1    Kirberger, M.2    Qiu, F.3    Chen, G.4    Yang, J.J.5
  • 35
    • 16344378407 scopus 로고    scopus 로고
    • Flexibility of metal binding sites in proteins on a database scale
    • Babor M, Greenblatt HM, Edelman M, Sobolev V. Flexibility of metal binding sites in proteins on a database scale. Proteins 2005; 59: 221-230.
    • (2005) Proteins , vol.59 , pp. 221-230
    • Babor, M.1    Greenblatt, H.M.2    Edelman, M.3    Sobolev, V.4
  • 36
    • 0032897494 scopus 로고    scopus 로고
    • An analysis of conformational changes on protein-protein association: implications for predictive docking
    • Betts MJ, Sternberg MJ. An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng 1999; 12: 271-283.
    • (1999) Protein Eng , vol.12 , pp. 271-283
    • Betts, M.J.1    Sternberg, M.J.2
  • 39
    • 77952728548 scopus 로고    scopus 로고
    • Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes
    • Wang X, Zhao K, Kirberger M, Wong H, Chen G, Yang JJ. Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes. Protein Sci 2010; 19: 1180-1190.
    • (2010) Protein Sci , vol.19 , pp. 1180-1190
    • Wang, X.1    Zhao, K.2    Kirberger, M.3    Wong, H.4    Chen, G.5    Yang, J.J.6
  • 40
    • 33749379347 scopus 로고    scopus 로고
    • Tomita E,Tanaka A,Takahashi H, editors. The worst-case time complexity for generating all maximal cliques, Heidelberg: Springer
    • Tomita E, Tanaka A, Takahashi H, editors. The worst-case time complexity for generating all maximal cliques, Vol. 3106. Heidelberg: Springer; 2004. pp 161-170.
    • (2004) , vol.3106 , pp. 161-170
  • 41
    • 84976668743 scopus 로고
    • Algorithm 457: finding all cliques of an undirected graph
    • Bron C, Kerbosch J. Algorithm 457: finding all cliques of an undirected graph. Commun ACM 1973; 16: 575-579.
    • (1973) Commun ACM , vol.16 , pp. 575-579
    • Bron, C.1    Kerbosch, J.2
  • 42
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: a new approach to ab initio protein structure prediction
    • Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003; 85: 1145-1164.
    • (2003) Biophys J , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 43
    • 79551476059 scopus 로고    scopus 로고
    • FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level
    • Brylinski M, Skolnick J. FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins 2011; 79: 735-751.
    • (2011) Proteins , vol.79 , pp. 735-751
    • Brylinski, M.1    Skolnick, J.2
  • 45
    • 67650150099 scopus 로고    scopus 로고
    • Improving structure-based function prediction using molecular dynamics
    • Glazer DS, Radmer RJ, Altman RB. Improving structure-based function prediction using molecular dynamics. Structure 2009; 17: 919-929.
    • (2009) Structure , vol.17 , pp. 919-929
    • Glazer, D.S.1    Radmer, R.J.2    Altman, R.B.3
  • 46
    • 84944648082 scopus 로고
    • Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides
    • Shannon RD. Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides. Acta Cryst A 1976; 32: 751-767.
    • (1976) Acta Cryst A , vol.32 , pp. 751-767
    • Shannon, R.D.1
  • 47
    • 0023156341 scopus 로고
    • Lead enters bovine adrenal medullary cells through calcium channels
    • Simons TJ, Pocock G. Lead enters bovine adrenal medullary cells through calcium channels. J Neurochem 1987; 48: 383-389.
    • (1987) J Neurochem , vol.48 , pp. 383-389
    • Simons, T.J.1    Pocock, G.2
  • 48
    • 0027439347 scopus 로고
    • Lead-protein interactions as a basis for lead toxicity
    • Goering PL. Lead-protein interactions as a basis for lead toxicity. Neurotoxicology 1993; 14: 45-60.
    • (1993) Neurotoxicology , vol.14 , pp. 45-60
    • Goering, P.L.1
  • 49
    • 0028332386 scopus 로고
    • The displacement of calcium from osteocalcin at submicromolar concentrations of free lead
    • Dowd TL, Rosen JF, Gundberg CM, Gupta RK. The displacement of calcium from osteocalcin at submicromolar concentrations of free lead. Biochim Biophys Acta 1994; 1226: 131-137.
    • (1994) Biochim Biophys Acta , vol.1226 , pp. 131-137
    • Dowd, T.L.1    Rosen, J.F.2    Gundberg, C.M.3    Gupta, R.K.4
  • 50
    • 0035313109 scopus 로고    scopus 로고
    • The biological chemistry of lead
    • Godwin HA. The biological chemistry of lead. Curr Opin Chem Biol 2001; 5: 223-227.
    • (2001) Curr Opin Chem Biol , vol.5 , pp. 223-227
    • Godwin, H.A.1
  • 51
    • 0043211858 scopus 로고    scopus 로고
    • Effects of toxic environmental contaminants on voltage-gated calcium channel function: from past to present
    • Atchison WD. Effects of toxic environmental contaminants on voltage-gated calcium channel function: from past to present. J Bioenerg Biomembr 2003; 35: 507-532.
    • (2003) J Bioenerg Biomembr , vol.35 , pp. 507-532
    • Atchison, W.D.1
  • 53
    • 0037040988 scopus 로고    scopus 로고
    • The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step
    • Asuncion M, Blankenfeldt W, Barlow JN, Gani D, Naismith JH. The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step. J Biol Chem 2002; 277: 8306-8311.
    • (2002) J Biol Chem , vol.277 , pp. 8306-8311
    • Asuncion, M.1    Blankenfeldt, W.2    Barlow, J.N.3    Gani, D.4    Naismith, J.H.5
  • 54
    • 84868211087 scopus 로고
    • Means AR, editor. Calcium regulation of celluar function,New York: Academic Press
    • Means AR, editor. Calcium regulation of celluar function, Vol. 30. New York: Academic Press; 1994.
    • (1994) , vol.30
  • 55
    • 0032189645 scopus 로고    scopus 로고
    • Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K
    • Singh TP, Sharma S, Karthikeyan S, Betzel C, Bhatia KL. Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K. Proteins 1998; 33: 30-38.
    • (1998) Proteins , vol.33 , pp. 30-38
    • Singh, T.P.1    Sharma, S.2    Karthikeyan, S.3    Betzel, C.4    Bhatia, K.L.5
  • 56
    • 50649111872 scopus 로고    scopus 로고
    • 2+-binding sites in proteins: implications with respect to toxicity
    • 2+-binding sites in proteins: implications with respect to toxicity. J Inorg Biochem 2008; 102: 1901-1909.
    • (2008) J Inorg Biochem , vol.102 , pp. 1901-1909
    • Kirberger, M.1    Yang, J.J.2
  • 57
    • 0027945446 scopus 로고
    • Molecular tuning of ion binding to calcium signaling proteins
    • Falke JJ, Drake SK, Hazard AL, Peersen OB. Molecular tuning of ion binding to calcium signaling proteins. Q Rev Biophys 1994; 27: 219-290.
    • (1994) Q Rev Biophys , vol.27 , pp. 219-290
    • Falke, J.J.1    Drake, S.K.2    Hazard, A.L.3    Peersen, O.B.4
  • 59
    • 76449084891 scopus 로고    scopus 로고
    • Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering
    • Yanyi C, Shenghui X, Yubin Z, Jie YJ. Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering. Sci China Chem 2010; 53: 52-60.
    • (2010) Sci China Chem , vol.53 , pp. 52-60
    • Yanyi, C.1    Shenghui, X.2    Yubin, Z.3    Jie, Y.J.4
  • 60
    • 37349120036 scopus 로고    scopus 로고
    • Prediction of transition metal-binding sites from apo protein structures
    • Babor M, Gerzon S, Raveh B, Sobolev V, Edelman M. Prediction of transition metal-binding sites from apo protein structures. Proteins 2008; 70: 208-217.
    • (2008) Proteins , vol.70 , pp. 208-217
    • Babor, M.1    Gerzon, S.2    Raveh, B.3    Sobolev, V.4    Edelman, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.