The 3-dimensional organisation of amino acids in a protein, specifically including the secondary, tertiary and quaternary structures.
Questions tagged [protein-structure]
184 questions
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How to identify a coiled coil from the amino acid sequence?
I was wondering, when we have an amino acid sequence, is it enough to check whether the positions a-d correspond to hydrophobic amino acids in order to say whether it can form a coiled coil structure? Or would we need to make sure the other…
Bee
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α-β Interfaces of Hemoglobin
I am trying to learn the interactions that hold the hemoglobin tetramer together, and the conformational changes induced at various allosteric sites. So far, what I know is this:
The tetramer can exist in relaxed state (R-state), or tense state…
Bob
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What is a "monomeric polypeptide"?
In the sentence: "Bacteriophage (viral) polymerases are typically monomeric polypeptides".
I know that polypeptides are chains of amino acids monomers. But what is a "monomeric polypeptide" and what other kinds of polypeptides are there?
clay
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What do ribbon diagrams mean?
What is the higher order meaning of ribbon diagrams like this one? I know the first order meaning is a graphical representation of α-helices and β-sheets, but what else does it mean? Is the protein's function or behavior encoded in there? Do the…
zencraft
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How do you biologists draw a protein when you write a paper?
The following is one example of protein structure diagram that I want to put in my research paper. I took this from
Koniev, O. & Wagner, A. “Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions…
chemrese
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Bonding in the primary structure of a protein
My textbook says:
The amino group of an amino acid reacts with the carbonyl group of another amino acid at the end of a polypeptide chain. This condensation reaction forms a peptide bond. ... The precise sequence of amino acids in a polypeptide…
Cyclopropane
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The meaning of atoms sign in protein structure
There are some atoms sign of protein structure in paper, like Nε2， Cε. I know this sign is for information about atoms position, but I don't know the exact meaning. The below is original words in paper, which is about structure of type3 copper…
Charlie Xiong
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Why is protein cyclisation desirable?
There are a number of methods to "cyclize" an existing peptide:
Disulphide bond as described in Disulfide Bond Mimetics: Strategies and Challenges by Gori et al.
"Linchpin" based (linker chemistry) as described in Synthetic Cross-linking of…
Seanny123
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Can the knowledge about torsion angles alone be sufficient for specifying secondary structures of protein?
I have read that Ramachandran plots are used to identify secondary structures of proteins. Also, alpha helices and beta strands cluster around specific regions of the plot which gives us the information about how much of these structures are present…
Noob
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Do the centrioles in the centrosome differ in their angle to one another?
The centrioles in the centrosome are often shown at an orthogonal angle, does this arrangement differ between samples, as in, does the daughter centriole show up in different sides of the mother centriole, or on the distal end rather than the…
m093
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Why glycosylation of a protein increases its non-specific binding properties?
This doubt arose while reading this website: https://www.thermofisher.com/cn/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/avidin-biotin-complex-method-ihc-detection.html
Indresh
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Does protein consist of repeating units of amino acids?
I am currently studying the chapter called macromolecule. I get that a nucleic acid consists of repeating units of nucleotides, and I personally think "the repeating units" does not mean the nucleotdes are all the same, as nitrogen bases have four…
Q.MEO
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Depositing/publishing protein structure simulations
Just wondering if anyone has any information on what the general consensus on publishing/depositing online protein structure simulations is?
I've been doing a fair bit of work to characterise the 'quality' of the simulations I have (how well they…
Joe Healey
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TBX3 Protein structure and function
Is it possible for an anti-cancer monoclonal antibody to target the two repressor domains in the N and C terminal of the TBX3 protein ?
Jennifer
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