Isolation and sequence-specific DNA binding of the Antennapedia homeodomain.

Müller, Martin; Affolter, Markus; Leupin, Werner; Otting, Gottfried; Wüthrich, Kurt; Gehring, Walter

doi:10.1002/j.1460-2075.1988.tb03328.x

Cited by 221 publications

(116 citation statements)

References 33 publications

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“…When more DNA fragments were bound to the sensor chip, the ability of the protein to gain access to the DNA could have been reduced by steric hindrance. It is known that the homeodomain binds to DNA in a monomeric form [8] (in this earlier study, the authors showed that, even if dimerization were to occur, the dissociation constant must be > 10 -4 M). It is also known that there is only one recognition sequence in the A element.…”

Section: Interactions Between the Antp Homeodomain And Threementioning

confidence: 90%

“…It is a polypeptide of 68 amino acids that includes the entire Antp homeodomain, with a serine residue at the 39th position replacing a cysteine residue. It was produced in E. coli and purified as described by MOiler et al [8]. Three kinds of 26 bp ds oligonucleotide, with one strand biotinylated at its terminus were synthesized chemically for this study.…”

Section: Preparation Of the Antp Homeodomain And Oligonucleotidesmentioning

confidence: 99%

“…1. One fragment, the A element, contained an authentic binding sequence for the Antp homeodomain [8]. The other two sequences, the N and M elements, contained an irrelevant sequence and a mutated sequence, respectively.…”

Section: Preparation Of the Antp Homeodomain And Oligonucleotidesmentioning

confidence: 99%

“…Each homeodomain that is encoded by a homeobox can bind specifically to a region of double-stranded (ds) DNA with a specific recognition sequence [2][3][4][5][6]. The interactions between homeodomains and DNA have been extensively analyzed by foot-printing methods and gel shift assays [6][7][8][9][10][11][12][13][14]. Direct structural analysis of the complexes has also been performed with NMR and X-ray [15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

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Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Seimiya¹,

Kurosawa²

1996

FEBS Letters

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The kinetics of binding of the Antp homeodomain to three kinds of DNA fragment were analyzed by measurements of surface plasmon resonance at various temperatures. Non-specific and specific binding of the homeodomain to DNA was examined. In the case of non-specific binding, the association rate constant (kass) was estimated to be 1.41-2.62X 105 M -1 s -1 and the dissociation rate constant (kdiss) was 1.36-3.10 X 10 -2 s -1, thus, the dissociation constant (KI)) was 0.847-1.72 × 10 7 M. The association seemed to be driven by entropy. In the case of specific binding, by contrast, the enthalpy term seemed to contribute more to the binding than did the entropy term. The kass was 2.04-2.59X105 M -1 s -1 and the kdiss was 0.759-1.16X10 -3 s -1, thus, the /to was 2.93-5.69X 10 -9 M. These values were measured under the condition of 150 mM NaCl. Both interactions were strongly dependent on the concentration of NaC1. The /to at 50 mM NaCI became several tens of times smaller than those at 150 mM. Possible reasons for the differences between non-specific and specific interactions are discussed.

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Section: Interactions Between the Antp Homeodomain And Threementioning

confidence: 90%

Section: Preparation Of the Antp Homeodomain And Oligonucleotidesmentioning

confidence: 99%

Section: Preparation Of the Antp Homeodomain And Oligonucleotidesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Seimiya¹,

Kurosawa²

1996

FEBS Letters

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“…This motif was first found in Drosophila homeotic and segmentation genes (McGinnis et al 1984;Scott & Weiner 1984) and subsequently in related genes in a wide variety of organisms including mammals, nematodes and plants (summarized by Kappen et al 1993). The homeobox encodes a homeodomain with their DNA binding activity (Muller et al 1988) which has a helix-turn-helix structure virtually identical to those observed for prokaryotic repressors (Qian et al 1989). More than one-hundred homeobox genes have so far been isolated from the mouse genome.…”

Section: Introductionmentioning

confidence: 93%

Expression of the Vax family homeobox genes suggests multiple roles in eye development

et al. 1999

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From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins

1996

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An improved scheme to help in the prediction of protein structure is presented. This procedure generates improved starting conformations of a protein suitable for energy minimization. Trivariate gaussian distribution functions for the π, ψ, and χ1 dihedral angles have been derived, using conformational data from high resolution protein structures selected from the Protein Data Bank (PDB). These trivariate probability functions generate initial values for the π, ψ, and χ1 dihedral angles which reflect the experimental values found in the PDB. These starting structures speed the search of the conformational space by focusing the search mainly in the regions of native proteins. The efficiency of the new trivariate probability distributions is demonstrated by comparing the results for the α‐class polypeptide fragment, the mutant Antennapedia (C39 → S) homeodomain (2HOA), with those from two reference probability functions. The first reference probability function is a uniform or flat probability function and the second is a bivariate probability function for π and ψ. The trivariate gaussian probability functions are shown to search the conformational space more efficiently than the other two probability functions. The trivariate gaussian probability functions are also tested on the binding domain of Streptococcal protein G (2GB1), an α/β class protein. Since presently available energy functions are not accurate enough to identify the most native‐like energy‐minimized structures, three selection criteria were used to identify a native‐like structure with a 1.90‐Å rmsd from the NMR structure as the best structure for the Antennapedia fragment. Each individual selection criterion (ECEPP/3 energy, ECEPP/3 energy‐plus‐free energy of hydration, or a knowledge‐based mean field method) was unable to identify a native‐like structure, but simultaneous application of more than one selection criterion resulted in a successful identification of a native‐like structure for the Antennapedia fragment. In addition to these tests, structure predictions are made for the Antennapedia polypeptide, using a Pattern Recognition‐based Importance‐Sampling Minimization (PRISM) procedure to predict the backbone conformational state of the mutant Antennapedia homeodomain. The ten most probable backbone conformational state predictions were used with the trivariate and bivariate gaussian dihedral angle probability distributions to generate starting structures (i.e., dihedral angles) suitable for energy minimization. The final energy‐minimized structures show that neither the trivariate nor the bivariate gaussian probability distributions are able to overcome the inaccuracies in the backbone conformational state predictions to produce a native‐like structure. Until highly accurate predictions of the backbone conformational states become available, application of these dihedral angle probability distributions must be limited to problems, such as homology modeling, in which only a limited portion of the backbone (e.g., surface loops) must b...

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Isolation and sequence-specific DNA binding of the Antennapedia homeodomain.

Cited by 221 publications

References 33 publications

Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance

Expression of the Vax family homeobox genes suggests multiple roles in eye development

From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins

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