Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
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Q-TOF vs Q-orbitrap MS data
I recently had the opportunity to analyze the same (intact protein) sample on an Agilent QTOF and a Thermo Q-Exactive, and noticed that in addition to having a moderately higher resolution the ...
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Loss of entropy and solvation energy in proteins
I am reading a chapter on protein stability. One section outlines the role of salt bridges or ion pairs in the stability of a protein. The excerpt goes as follows (italization added for emphasis):
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What do sequence numbers in PDB files actually mean and why don't they match the sequence?
I am studying the 3D structure of the LDH from x-ray crystallographic imaging I was pointed to from Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry ...
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Hypothetical Alternative for Nitrogen [closed]
Recently I was surfing the internet and I found thisWikipedia article.
It states that
The element silicon has been much discussed as a hypothetical alternative to carbon. Silicon is in the same group ...
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What is "tail" in case of secondary structure of protein? [closed]
What is a "tail" in the case of the secondary structure of a protein?
How does it influence the "protein assignment" task?
user93950
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2
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How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?
So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
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How can all amino acids point outwards from an alpha helix, if peptides are mostly trans?
My textbook in biochemistry ("Biochemistry" - Berg,Tymoczom Gatto, Stryer) tells me that:
"Almost all peptide bonds in proteins are trans" (p. 40)
At the same time, it states the ...
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Lysozyme crystals versus NaCl
If someone has some experience with lysozyme crystals I would be interested in knowing whether any of the images below seem likely to be lysozyme. Solutions were made with powdered lysozyme ($\pu{50 ...
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What do natural hybrids of peptides and nucleic acids look like?
Until recently I thought that there was a clean distinction between polypeptides and oligonucleotides, but apparently there are recent studies of therapeutic compounds that could be described as "...
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What does it mean by spatial neighbor?
What does it mean by a spatial neighbor (SN) in the case of a protein residue or protein chain?
Why is it different or special as opposed to other neighbors?
user93950
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What is the maximum length of peptide which considered to be hard for synthesis by the current technology?
I am a molecular biologist and work with recombinant proteins. I am wondering what the cut point, in terms of length, is at which I should produce the peptide using heterologous expression rather than ...
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How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?
When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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What does the following diagram represent?
Suppose, the following is a diagram of a protein's polypeptide chain:
What does this diagram represent?
What are the letters A, E, M, W, L, N, S, etc. represent? (I suppose these are amino acid ...
user93950
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Can Amphotericin B cross a lipid bilayer membrane in its zwitterionic form when it is loaded in the aqueous core of a liposome?
Can Amphotericin B cross a lipid bilayer membrane in its zwitterionic form when it is loaded in the aqueous core of a liposome? Or must it be uncharged in order to cross the lipid bilyer membrane of ...
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Protein drug conjugate exercise
I am supposed to draw the structure of a derivative of the following structure which could be used to make a protein drug conjugate. And then I should draw the reaction for the protein modification.
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