Mapping antibody binding sites on cytochrome c
 with synthetic peptides: Are results representative of the antigenic structure of proteins?

The multifunctional DNA-binding proteins ABF1 and CPF1 bind in a mutually exclusive manner to the promoter region of the QCR8 gene, which encodes 11-kDa subunit VIII of the Saccharomyces cerevisiae mitochondrial ubiquinol-cytochrome c oxidoreductase (QCR). We investigated the roles that the two factors play in transcriptional regulation of this gene. To this end, the overlapping binding sites for ABF1 and CPF1 were mutated and placed in the chromosomal context of the QCR8 promoter. The effects on transcription of the QCR8 gene were analyzed both under steady-state conditions and during nutritional shifts. We found that ABF1 is required for repressed and derepressed transcription levels and for efficient induction of transcription upon escape from catabolite repression, independently of DNA replication. CPF1 acts as a negative regulator, modulating the overall induction response. Alleviation of repression through CPF1 requires passage through the S phase. Implications of these findings for the roles played by ABF1 and CPF1 in global regulation of mitochondrial biogenesis are discussed.

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The intrinsic cysteine and histidine residues of the anti-Salmonella antibody Se155-4: a model for the introduction of new functions into antibody-binding sites

Protein Engineering Design and Selection ◽

10.1093/protein/gzu018 ◽

2014 ◽

Vol 27 (10) ◽

pp. 383-390 ◽

Cited By ~ 3

Author(s):

N. M. Young ◽

D. C. Watson ◽

A. M. Cunningham ◽

C. R. MacKenzie

Keyword(s):

Binding Sites ◽

Antibody Binding ◽

Histidine Residues

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New Light on the T-Cell Receptor in Relation to Antibody Binding Sites

Investigation and Exploitation of Antibody Combining Sites ◽

10.1007/978-1-4684-5006-4_31 ◽

1985 ◽

pp. 277-278

Author(s):

E. S. Golub

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Binding Sites ◽

Cell Receptor ◽

Antibody Binding

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Molecular dynamics approach for capturing calixarenes--proteins interactions: the case of cytochrome c

10.26434/chemrxiv.11903112 ◽

2020 ◽

Author(s):

Alessio Bartocci ◽

florence szczepaniak ◽

Tao Jiang ◽

Natacha Gillet ◽

Elise Dumont

Keyword(s):

Molecular Dynamics ◽

Cytochrome C ◽

Binding Sites ◽

Supervised Machine Learning ◽

Titration Calorimetry ◽

X Ray ◽

Poisson Boltzmann ◽

Bond Network ◽

Proteins Interactions ◽

Detailed Picture

Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonatedcalix-[8]-arenes to cytochrome c. The binding sites prone to interactions with sulfonated calixarenescan be identified without prior knowledge of the X-ray structure, and the binding free energiesestimated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) post-analysis arefound to be in neat agreement with the isothermal titration calorimetry (ITC) measurements The per-residuedecomposition reveals the detailed picture of this electrostatically-driven association and notably therole of the arginine R13 as a bridge residue between the two main anchoring sites. In addition,the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of theprotein.

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