Home LiteratureArticle Details
PMID: 11420431 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers.

Protein science : a publication of the Protein Society ·Vol. 10 ·No. 7 ·2001-07-00 ·Pages 1293-304

Green NS, Reisler E, Houk KN

Abstract

Homobifunctional chemical cross-linking reagents are important tools for functional and structural characterization of proteins. Accurate measures of the lengths of these molecules currently are not available, despite their widespread use. Stochastic dynamics calculations now provide quantitative measures of the lengths, and length dispersions, of 32 widely used molecular rulers. Significant differences from published data have been found. See www.proteinscience.org

MeSH Terms
Amines/chemistry Cross-Linking Reagents/chemistry Models, Molecular Molecular Conformation Molecular Structure Proteins/chemistry Stochastic Processes Sulfhydryl Compounds/chemistry
Chemicals
Amines Cross-Linking Reagents Proteins Sulfhydryl Compounds
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Green N S
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569, USA.
Reisler E
Houk K N
References (102)
102 references, click to expand
  1. Chemical cross-linking reveals a dimeric structure for CTP:phosphocholine cytidylyltransferase.
    J Biol Chem. 1989 May 25;264(15):9077-82 PMID: 2542297
  2. Control of cell membrane ecto-ATPase by oligomerization state: intermolecular cross-linking modulates ATPase activity.
    Biochemistry. 1996 Jun 25;35(25):8289-98 PMID: 8679585
  3. A method for isolation and purification of specific antibodies to a protein fused to the GST.
    Anal Biochem. 1996 Oct 1;241(1):140-2 PMID: 8921178
  4. The preparation of a chemically cross-linked complex of the basic pancreatic trypsin inhibitor with trypsin.
    Biochemistry. 1974 Feb 12;13(4):698-702 PMID: 4855764
  5. Activity in monomers of human cytomegalovirus protease.
    Biochem Biophys Res Commun. 1999 Jun 7;259(2):370-3 PMID: 10362516
  6. Cross-linking of bovine pancreatic ribonuclease A with dimethyl adipimidate.
    Biochemistry. 1967 Aug;6(8):2439-48 PMID: 6049468
  7. Cross-linking of troponin with dimethylimido esters.
    Biochemistry. 1975 Nov 18;14(23):5162-7 PMID: 811252
  8. The specific cross-linking of two proteins from the Escherichia coli 30 s ribosomal subunit.
    J Mol Biol. 1972 Jul 14;68(1):177-80 PMID: 4559111
  9. Cytotoxicity of a hybrid prepared by coupling diphtheria toxin A-chain with immunoglobulin Fab' with N,N'-o-phenylenedimaleimide.
    Biochem Biophys Res Commun. 1981 Sep 16;102(1):561-7 PMID: 7306286
  10. Site-directed spin labeling and chemical crosslinking demonstrate that helix V is close to helices VII and VIII in the lactose permease of Escherichia coli.
    Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10123-7 PMID: 8816762
  11. Cross-linking of the ryanodine receptor/Ca2+ release channel from skeletal muscle.
    Biochim Biophys Acta. 1995 Jul 26;1237(2):151-61 PMID: 7632708
  12. Delta subunit of rat liver mitochondrial ATP synthase: molecular description and novel insights into the nature of its association with the F1-moiety.
    Biochemistry. 1998 May 12;37(19):6911-23 PMID: 9578578
  13. Cross-linking induces homodimer formation and inhibits enzymatic activity of chicken stomach ecto-apyrase.
    Biochem Mol Biol Int. 1998 Mar;44(3):463-70 PMID: 9556206
  14. Characterization of chemically crosslinked human factor VIIIa.
    Biochem Biophys Res Commun. 1994 Apr 15;200(1):233-8 PMID: 8166691
  15. Bovine serum albumin: characterization of a fatty acid binding site on the N-terminal peptic fragment using a new spin-label.
    Biochemistry. 1984 Dec 4;23(25):5930-2 PMID: 6098304
  16. Importance of the antigen-binding valency and the nature of the cross-linking bond in ricin A-chain conjugates with antibody.
    J Biochem. 1982 May;91(5):1583-91 PMID: 7096308
  17. Use of cross-linking reagents to study lipoprotein structure.
    Methods Enzymol. 1986;128:613-26 PMID: 3724526
  18. Use of a diimidoester cross-linking reagent to examine the subunit structure of rabbit muscle pyruvate kinase.
    Can J Biochem. 1972 Apr;50(4):416-22 PMID: 5063715
  19. Structural interactions between retroviral Gag proteins examined by cysteine cross-linking.
    J Virol. 1995 Feb;69(2):1150-9 PMID: 7815493
  20. Identification of residues in the drug-binding site of human P-glycoprotein using a thiol-reactive substrate.
    J Biol Chem. 1997 Dec 19;272(51):31945-8 PMID: 9405384
  21. Chemical cross-linking indicates a staggered and antiparallel protofilament of desmin intermediate filaments and characterizes one higher-level complex between protofilaments.
    Eur J Biochem. 1992 Jun 15;206(3):841-52 PMID: 1606966
  22. Analysis of the interaction between properdin and factor B, components of the alternative-pathway C3 convertase of complement.
    Biochem J. 1988 Aug 1;253(3):667-75 PMID: 3140783
  23. Characterization of a C5a receptor on human polymorphonuclear leukocytes (PMN).
    J Immunol. 1985 Sep;135(3):2063-8 PMID: 4020139
  24. Radiohalogenation of proteins: an overview of radionuclides, labeling methods, and reagents for conjugate labeling.
    Bioconjug Chem. 1992 Nov-Dec;3(6):433-70 PMID: 1463775
  25. Species differences in the molecular characteristics of vasoactive-intestinal-peptide receptors in the pancreas from rat and guinea-pig.
    Eur J Biochem. 1988 May 16;174(1):59-66 PMID: 2836201
  26. Identification of residues in the drug-binding domain of human P-glycoprotein. Analysis of transmembrane segment 11 by cysteine-scanning mutagenesis and inhibition by dibromobimane.
    J Biol Chem. 1999 Dec 10;274(50):35388-92 PMID: 10585407
  27. Fixation of allosteric states of the nicotinic acetylcholine receptor by chemical cross-linking.
    Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):8202-7 PMID: 9223339
  28. Characterization of high-affinity receptors for interleukin 5 on interleukin 5-dependent cell lines.
    Proc Natl Acad Sci U S A. 1989 Apr;86(7):2311-5 PMID: 2784567
  29. Biochemical studies on oral toxicity of ricin. V. The role of lectin activity in the intestinal absorption of ricin.
    Chem Pharm Bull (Tokyo). 1992 May;40(5):1216-20 PMID: 1394637
  30. The formation of a crosslinked carboxyhemoglobin membrane at an organic-aqueous interface.
    Artif Cells Blood Substit Immobil Biotechnol. 1996 May;24(3):185-96 PMID: 8773738
  31. The myosin SH2-50-kilodalton fragment cross-link: location and consequences.
    Biochemistry. 1988 Mar 8;27(5):1778-85 PMID: 3365423
  32. Thiol cross-linking of cytoplasmic loops in the lactose permease of Escherichia coli.
    Biochemistry. 2000 Mar 21;39(11):3134-40 PMID: 10715135
  33. The agonist binding site on the bovine bradykinin B2 receptor is adjacent to a sulfhydryl and is differentiated from the antagonist binding site by chemical cross-linking.
    J Biol Chem. 1995 Sep 1;270(35):20591-8 PMID: 7657637
  34. A label selection procedure for determining the location of protein-protein interaction sites by cross-linking with bisimidoesters. Application to lactose synthase.
    J Biol Chem. 1981 May 10;256(9):4193-204 PMID: 6783656
  35. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry.
    Anal Chem. 2000 Jan 15;72(2):267-75 PMID: 10658319
  36. Cross-linking of human 125I-beta-endorphin to a mu-delta opioid receptor complex in rat striatum.
    Eur J Pharmacol. 1989 Jul 18;166(2):357-8 PMID: 2551701
  37. Cross-linked trimers of bovine ribonuclease A: activity on double-stranded RNA and antitumor action.
    FEBS Lett. 1997 Oct 6;415(3):308-12 PMID: 9357989
  38. Influence of nucleotide on chemical crosslinking between alkali light chains and the heavy chain of myosin subfragment 1.
    Biochim Biophys Acta. 1990 Aug 1;1040(1):89-94 PMID: 2378906
  39. Chemical cross-linking: reagents and problems in studies of membrane structure.
    Annu Rev Biochem. 1977;46:523-51 PMID: 409338
  40. Molecular characteristics and evidence for internalization of vasoactive-intestinal-peptide (VIP) receptors in the tumoral rat-pancreatic acinar cell line AR 4-2 J.
    Eur J Biochem. 1988 Oct 1;176(3):707-13 PMID: 2844535
  41. A clonal rat pancreatic delta cell line (Rin14B) expresses a high number of galanin receptors negatively coupled to a pertussis-toxin-sensitive cAMP-production pathway.
    Eur J Biochem. 1991 Jan 30;195(2):459-63 PMID: 1847683
  42. Photochemical cross-linking of cell membranes. A test for natural and random collisional cross-links by millisecond cross-linking.
    J Biol Chem. 1977 Dec 10;252(23):8524-31 PMID: 925009
  43. Inactivation of glyceraldehyde 3-phosphate dehydrogenase by a bifunctional reagent.
    FEBS Lett. 1969 Oct 21;5(2):153-156 PMID: 11947264
  44. Modification of specific lysine residues in E. coli methionyl-tRNA synthetase by crosslinking to E. coli formylmethionine tRNA.
    Biochem Biophys Res Commun. 1984 Mar 15;119(2):677-84 PMID: 6424668
  45. Probing the conformational states of the SH1-SH2 helix in myosin: a cross-linking approach.
    Biochemistry. 1998 Nov 24;37(47):16704-10 PMID: 9843439
  46. Organization of the transcortin-binding domain on placental plasma membranes.
    Biochim Biophys Acta. 1995 May 4;1235(2):387-94 PMID: 7756349
  47. Characterization of molecular aggregates of alpha 1 beta 1-integrin and other rat liver membrane proteins by combination of size-exclusion chromatography and chemical cross-linking.
    J Chromatogr A. 1995 Sep 8;711(1):187-99 PMID: 7496490
  48. Atomic model of the actin filament.
    Nature. 1990 Sep 6;347(6288):44-9 PMID: 2395461
  49. Bifunctional reagents for the crosslinking of proteins.
    Angew Chem Int Ed Engl. 1971 Nov;10(11):795-801 PMID: 5001715
  50. Species specificity of human and murine tumor necrosis factor. A comparative study of tumor necrosis factor receptors.
    J Biol Chem. 1986 Nov 15;261(32):14871-4 PMID: 3021754
  51. Self-association of the globular domain of histone H5.
    Biochemistry. 1994 Feb 15;33(6):1300-10 PMID: 8312247
  52. Subunit interactions in the clathrin-coated vesicle vacuolar (H(+))-ATPase complex.
    J Biol Chem. 1999 Oct 8;274(41):28909-15 PMID: 10506135
  53. Solubilization and molecular characterization of active galanin receptors from rat brain.
    Biochemistry. 1992 Mar 3;31(8):2415-22 PMID: 1371697
  54. Modification of hemoglobin S with dimethyl adipimidate. Contribution of individual reacted subunits to changes in properties.
    Biochim Biophys Acta. 1982 Jun 24;704(3):389-97 PMID: 7115723
  55. D-glucose metabolism in dimethyl suberimidate-treated tumoral pancreatic islet cells.
    Biochem Mol Biol Int. 1997 May;41(6):1209-16 PMID: 9161716
  56. Synthesis and biochemical characterization of obligatory dimers of the sugar non-specific nuclease from Serratia marcescens using specifically designed bismaleimidoalkanes as SH-specific crosslinking reagents.
    J Protein Chem. 1999 Jan;18(1):137-46 PMID: 10071938
  57. Cross-linking of myosin subfragment 1. Nucleotide-enhanced modification by a variety of bifunctional reagents.
    J Biol Chem. 1980 Dec 10;255(23):11135-40 PMID: 7440533
  58. Differential affinity cross-linking of phosphorylase kinase conformers by the geometric isomers of phenylenedimaleimide.
    J Biol Chem. 1997 Oct 17;272(42):26196-201 PMID: 9334187
  59. Molecular associations of IA antigens after T-B cell interactions. I. Identification of new molecular associations.
    J Immunol. 1988 Aug 15;141(4):1252-60 PMID: 2456348
  60. Structure of the murine erythropoietin receptor complex. Characterization of the erythropoietin cross-linked proteins.
    J Biol Chem. 1991 Dec 5;266(34):23380-5 PMID: 1660472
  61. Molecular characterization and peptide specificity of two vasoactive intestinal peptide (VIP) binding sites in the chicken pineal.
    Neuropeptides. 1991 May;19(1):1-8 PMID: 1653910
  62. Stabilization of restriction endonuclease Bam HI by cross-linking reagents.
    Biotechnol Bioeng. 1989 Apr 20;33(10):1311-6 PMID: 18587865
  63. Characterization of the receptor to vasculotropin on bovine adrenal cortex-derived capillary endothelial cells.
    J Biol Chem. 1990 Dec 25;265(36):22071-4 PMID: 2266109
  64. Comparative cross-linking study on the 50S ribosomal subunit from Escherichia coli.
    Biochemistry. 1989 May 2;28(9):4099-105 PMID: 2665813
  65. Identification of opioid-binding materials of rat brain.
    Chem Pharm Bull (Tokyo). 1990 Jan;38(1):168-71 PMID: 2159852
  66. Cross-linking of erythrocyte membranes with dimethyl adipimidate.
    Biochim Biophys Acta. 1970;196(2):170-5 PMID: 5414302
  67. Structure and arrangement of the regulatory subunits in aspartate transcarbamylase.
    Biochemistry. 1972 Aug 29;11(18):3396-411 PMID: 4560264
  68. Specific interchain cross-linking of antibodies using bismaleimides. Repression of ligand leakage in immunoaffinity chromatography.
    Bioconjug Chem. 1991 Jul-Aug;2(4):275-80 PMID: 1772910
  69. Affinity labelling of endothelin receptor and characterization of solubilized endothelin-endothelin-receptor complex.
    Eur J Biochem. 1990 Jan 12;187(1):125-9 PMID: 2153541
  70. Refinement of the F-actin model against X-ray fiber diffraction data by the use of a directed mutation algorithm.
    J Mol Biol. 1993 Dec 5;234(3):826-36 PMID: 8254675
  71. The N terminus of bradykinin when bound to the human bradykinin B2 receptor is adjacent to extracellular Cys20 and Cys277 in the receptor.
    J Biol Chem. 1996 Nov 22;271(47):29746-51 PMID: 8939910
  72. Structural analysis of human immunodeficiency virus type 1 Gag protein interactions, using cysteine-specific reagents.
    J Virol. 1996 Aug;70(8):5106-14 PMID: 8764018
  73. The Na/Ca-K exchanger of rod photoreceptor exists as dimer in the plasma membrane.
    Biochemistry. 1997 Nov 4;36(44):13667-76 PMID: 9354636
  74. Interaction of non-histone proteins HMG1 and HMG2 with core histones in nucleosomes and core particles revealed by chemical cross-linking.
    Eur J Biochem. 1987 Jan 2;162(1):111-8 PMID: 3816775
  75. Consequences of placing an intramolecular crosslink in myosin S1.
    Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1461-6 PMID: 10677484
  76. Helix packing in the lactose permease of Escherichia coli determined by site-directed thiol cross-linking: helix I is close to helices V and XI.
    Biochemistry. 1999 Mar 9;38(10):3120-6 PMID: 10074366
  77. The actin monomers in the ternary gelsolin: 2 actin complex are in an antiparallel orientation.
    Eur J Biochem. 1993 Dec 1;218(2):507-13 PMID: 8269940
  78. Characterization of the properties of ethenoadenosine nucleotides bound or trapped at the active site of myosin subfragment 1.
    Biochemistry. 1984 Aug 14;23(17):3994-4002 PMID: 6237680
  79. The distance between thiol groups in the gamma subunit of coupling factor 1 influences the proton permeability of thylakoid membranes.
    J Bioenerg Biomembr. 1982 Dec;14(5-6):347-59 PMID: 6298195
  80. The reactive SH1 and SH2 cysteines in myosin subfragment 1 are cross-linked at similar rates with reagents of different length.
    Biochem Biophys Res Commun. 1982 May 14;106(1):117-22 PMID: 6213228
  81. Nearest-neighbor analysis of higher-plant photosystem I holocomplex.
    Plant Physiol. 1996 Sep;112(1):409-20 PMID: 8819335
  82. Mapping the oligomeric interface of diacylglycerol kinase by engineered thiol cross-linking: homologous sites in the transmembrane domain.
    Biochemistry. 2000 Apr 11;39(14):4154-64 PMID: 10747807
  83. Rotavirus protein rearrangements in purified membrane-enveloped intermediate particles.
    J Virol. 1991 Sep;65(9):4720-7 PMID: 1651404
  84. Mapping of the region of the heavy chain of myosin subfragment 1 that can be crosslinked to the alkali light chains.
    Biochem Mol Biol Int. 1993 Oct;31(2):381-8 PMID: 8275027
  85. Proximity of periplasmic loops in the lactose permease of Escherichia coli determined by site-directed cross-linking.
    Biochemistry. 1997 Sep 30;36(39):11959-65 PMID: 9305990
  86. The proximity of the C-terminal domain of Escherichia coli ribosomal protein L7/L12 to L10 determined by cysteine site-directed mutagenesis and protein-protein cross-linking.
    J Biol Chem. 1992 Mar 25;267(9):5889-96 PMID: 1556104
  87. A new class of bradykinin antagonists: synthesis and in vitro activity of bissuccinimidoalkane peptide dimers.
    J Med Chem. 1992 May 1;35(9):1563-72 PMID: 1578482
  88. The quaternary geometry of transcription termination factor rho: assignment by chemical cross-linking.
    J Mol Biol. 1997 Jun 20;269(4):514-28 PMID: 9217257
  89. Intra- and inter-complex cross-linking of subunits in the quinol oxidase super-complex from thermophilic Bacillus PS3.
    J Biochem. 1996 Mar;119(3):482-6 PMID: 8830043
  90. The chloroplast cytochrome b 6 f complex can exist in monomeric and dimeric states.
    Photosynth Res. 1991 May;28(2):59-68 PMID: 24414859
  91. Cross-linking study on skeletal muscle actin: properties of suberimidate-treated actin.
    J Biochem. 1982 Jun;91(6):1999-2012 PMID: 7118859
  92. The reaction of 4,4'-difluoro-3,3'-dinitro-diphenyl sulfone with gamma-globulin and horseradish peroxidase.
    Biochim Biophys Acta. 1971 Feb 16;229(2):384-95 PMID: 5102878
  93. SAP97 is associated with the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR1 subunit.
    J Biol Chem. 1998 Jul 31;273(31):19518-24 PMID: 9677374
  94. Chemical crosslinking of alpha subunits in the F1 adenosine triphosphatase of Escherichia coli.
    Arch Biochem Biophys. 1986 Jan;244(1):361-72 PMID: 2868692
  95. Stabilization of human prostate acid phosphatase by cross-linking with diimidoesters.
    Acta Biochim Pol. 1987;34(2):145-56 PMID: 3673438
  96. Kinetic investigation of the ligand dependence of rabbit skeletal muscle myosin subfragment 1 Cys-697 and Cys-707 reactivities.
    Biochemistry. 1997 Sep 30;36(39):11952-8 PMID: 9305989
  97. Preparation and characterization of bifunctional biopolymers for receptor-based liposomal immunosensing.
    Biotechnol Prog. 1998 Mar-Apr;14(2):310-7 PMID: 9548785
  98. Thiol-specific cross-linkers of variable length reveal a similar separation of SH1 and SH2 in myosin subfragment 1 in the presence and absence of MgADP.
    Biochemistry. 1999 Aug 10;38(32):10307-17 PMID: 10441124
  99. The accessible surface of the nicotinic acetylcholine receptor. Identification by chemical modification and cross-linking with 14C-dimethyl suberimidate.
    Eur J Biochem. 1998 Mar 1;252(2):222-8 PMID: 9523692
  100. Dibromobimane as a fluorescent crosslinking reagent.
    Anal Biochem. 1995 Feb 10;225(1):174-6 PMID: 7778775
  101. Spatial proximity of Cys113, Cys172, and Cys422 in the metalloactivation domain of the ArsA ATPase.
    J Biol Chem. 1996 Oct 4;271(40):24465-70 PMID: 8798705
  102. Mechanism of the microtubule GTPase reaction.
    J Biol Chem. 1990 May 25;265(15):8935-41 PMID: 2160472
Article Info
Journal
Protein science : a publication of the Protein Society
Abbr.
Protein Sci
ISSN
0961-8368
Published
2001-07-00
Pages
1293-304
Language
English
Region
United States
NLM ID
9211750
PMCID
PMC2374107
Subset
IM
Grants
NIAMS NIH HHS · R01 AR022031 · United States
NIGMS NIH HHS · R01 GM061402 · United States
NIAMS NIH HHS · AR 22031 · United States
NIGMS NIH HHS · GM 61402 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com