Questions tagged [binding-sites]
Binding sites are sites in proteins or on DNA where other proteins or DNA can bind. Binding sites are usually conserved.
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Binding modes of a protein on a planar surface graphene
Can a protein have different binding modes on a flat even surface like graphene? For a surface like Graphene oxide I can understand, since it has several oxygenated groups on its surface that makes it ...
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DnaA binding energy to E coli genome
I have been told that DnaA binds strongly to DnaA boxes on the E coli genome, but binds weakly to 8 out of 11 sites near ori. I want to know more quantitatively what strongly and weekly mean. Are ...
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Binding BSA to silver surface via large difference in isoelectric points of the two materials
I would like to bind BSA to a silver surface so that I can utilize plasmonic sensing to detect the BSA. There seems to be two methods of doing this: 1) to rely on electrostatic forces or 2) to form a ...
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Is there a way to determine corresponding differential equations from fitted Hill equation parameters
I am currently doing some work with GCaMP, a genetically encoded calcium indicator. According to the literature the Hill equation parameters for GCaMP6m is $K_d=167\pm3\, \text{nM}$ and $n=2.96\pm0.04$...
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What kind of bonds are there between a Transcription Factor and its DNA binding site?
I want to know what kind of bonds are there between a Transcription Factor and its DNA binding site when the complex is created. This information will be used to determine the method for a molecular ...
user53283
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What is the active site (not metal binding site) of tyrosinase and other monooxygenase/oxidoreductases?
On https://www.uniprot.org/uniprot/P07524, tyrosinase is shown as a monophenol monooxygenase. However, the UniProt database only shows a metal (copper) binding site, when there is presumed to be an ...
user31285
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What is allele-specific binding?
So far all I have found is this:
https://www.biostars.org/p/132527/
My guess is that some alleles, for whatever reason, bind to things like transcription factors 'moreso' (for want of better word - ...
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Definition of nucleotide-associated proteins and RNA-polymerase associated proteins
Nucleotide-associated proteins and RNA-polymerase associated proteins, I found those two terms in an article but I didn't ...
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What makes DNA sequences most different/recognizable from a biological perspective? [duplicate]
We can pretty easily quantify the amount difference between two different strings/sequences of characters. For example, if we take the words trebuchet and trebucket, we can say they have a Levenshtein ...
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identifying which SNPs sit in TFBS (Yeast)
i have a set of ~11k SNPs for Saccharomyces cerevisiae, baker's yeast and i would like to identify which ones of these sit in transcription factor binding sites and if they do information on the ...
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How important is non-binding site of protein?
Just a curious question:
What will happen if i remove most protein sequence that encoded for non-binding site of Restriction Enzyme to make a new enzyme, can the new restriction enzyme still work?
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Location of TFBS in genome
I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether ...
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How much does the distance between a transcription factor binding site and a promoter influence transcription?
Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
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How can promoter binding sites be determined?
I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it ...
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variation in antigen binding site of antibodies
Antibodies or immunoglobulins are proteins made by the immune system in response to alien(!) molecules. Each antibody binds to its specific antigen. This great diversity and specificity is cause of ...
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ChIP-seq vs ChIP-exo
I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites.
As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...
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What is the correct model for enzyme-substrate complementarity?
This Wikibook shows both proposed models of enzyme-substrate complementarity, the Lock and Key model and the Induced Fit model. I've always been taught that the Induced Fit model is the proper one. ...
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determining genome-wide exogenous binding of pathogens to host genome?
I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice ...
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What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?
In prokaryotic translation, how critical for efficient translation is the location of the ribosome binding site, relative to the start codon?
Ideally, it is supposed to be -7b away from the start. ...
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