I want to design peptides probes with fluorescent moieties labelled for detecting biomolecules.
On what basis or experiments are you saying that peptides don't behave the same way.
This will help me in providing you with an appropriate solution that suits your need.
Just to add to whatever has been said. Small peptides are generally not structured in solution whereas in a protein they are structured, with help from other residues. This changes lot of things.
Hope this was what you were looking for.
I am not quite sure of your question. However it sounds like you are asking why a synthetic peptide based on the sequence of a ligand binding site does not behave the same way as the intact protein. There are several reasons for this. First, the actual ligand binding site may not encompass a linear sequence of amino acids. Amino acid residues that are far apart in the primary structure of a protein or polypeptide are brought into close proximity of each other (and in the correct spatial orientation) to form a binding site through the folding of the protein. In other words, the entire protein serves as a scaffold to hold the amino acids responsible for ligand binding in the correct orientation to make up the binding site. If the binding site is indeed encompassed in a linear sequence, there still may not be enough defined structure to the short peptide fragment for it to interact productively with the ligand.
However, if you are looking to design peptide probes to detect biomolecules then these should be based on peptides known to interact with the target protein. If they are not working/binding then you may want to address the following questions. Do you have the correct sequence? Is the sequence long enough for binding? Has the structure of the peptide been confirmed by mass spec or NMR analysis? Also keep in mind that placement of the reporter group (fluorescent tag) can also be important. If the fluorophore is too bulky it may inhibit binding of the ligand through steric hindrance. Some trial and error may be needed to find the optimal placement of fluorophore.
On what basis or experiments are you saying that peptides don't behave the same way.
This will help me in providing you with an appropriate solution that suits your need.
Just to add to whatever has been said. Small peptides are generally not structured in solution whereas in a protein they are structured, with help from other residues. This changes lot of things.
Hope this was what you were looking for.
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