Questions tagged [proteins]

Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.

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What is the thickness of the membrane if only alpha helixes are embedded of a transmembrane protien?

Given is the representation of a transmembrane protein. Calculate the thickness of the membrane if only alpha helixes are embedded in it. One turn = 5.4Å
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Which enzymes use ATP?

It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well ...
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Western blotting: what common tweaks do you make to the protocol and why would you make membrane cuts?

I'm building an app which helps researchers plan out Western blots, record protocol tweaks and receive warnings in the app if: you're trying to multiplex antibodies of similar molecular weight on the ...
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69 views

Calculating sequence divergence score for a protein from identity or similarity score?

I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue ...
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What are the effect of radioactivity on grey wolves in Chernobyl?

I am doing some research about the effects that radioactivity has and is having on grey wolves in Chernobyl and more particularly on their genetics, but maybe also looking at the populations in the ...
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Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles

First Question : RNA interference - small-interference RNA in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin this Figure is Shown my question is : if the foreign RNA ...
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Does hydrolysis of carbohydrates, proteins, and fats occur in the small intestine?

Does the hydrolysis of carbohydrates, proteins, and fats occur in the small intestine? I have researched this and just cannot seem to get a clear-cut answer. Perhaps I am misunderstanding something? ...
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What happens when you mix catalase found in yeast with a small, medium, and large amount of isopropyl alcohol and hydrogen peroxide?

I conducted an experiment trying to see what isopropyl alcohol does to the catalase found in yeast's catalytic activity. I can not make sense of the results which showed that a 1:10 ratio and 1:1 ...
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Why can't plain water be used in dialysis? Why is buffer used?

I read that buffer is used in dialysis because usage of water could cause precipitation of proteins but I don't really understand why and how water can cause precipitation of proteins and buffer ...
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Are there any online resources for finding the signaling pathways that two proteins both belong to?

I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these ...
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What does ΔC and ΔN mean with regards to a protein sequence?

I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement: Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the amino-...
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Do we find protein not of cellular origin in nature?

I read once that we have two sources for proteins: Protein that is made in cells Protein that is made in labs However, based on Miller–Urey experiment, it's argued that amino acids can be made from ...
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Did Mendel believe that proteins are hereditary substances?

Scientists first thought that proteins, which are found in chromosomes along with DNA, would turn out to be the sought-after genetic material. Proteins were known to have diverse amino acid sequences, ...
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Is there any commercial vector technology platform for boosting recombinant protein production?

I am a novice in biomedical industry. Our team would like to search new vector technology for boosting recombinant protein production. It's difficult to google a firm that provide those plasmids. Dose ...
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Predicting how proteins will be cleaved

Is it possible to predict how proteins coded from mRNA will be cleaved? The reason I was interested in this is because I did some initial work to translate the raw Coronavirus RNA sequences, which you ...
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How does the eukaryotic cell synthesize all of the proteins of a protein complex (like ETC complex I) at stoichiometric ratios/numbers? [closed]

(eg synthesize all proteasome proteins at the appropriate ratios to which they are used) How often are proteins of the same complex (eg all the proteins of the 20S/19S parts of the proteasome or ...
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Speed of protein conformational change?

Although the speed may vary a lot based on factors like protein size/scale of conformational change/type of changes (small block change/arm movement,etc), are there examples of experimental results of ...
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Why can't C1r cleave C4 proteins?

I am researching the complement system, and have ran into something I'm not really sure about. In the past, the C1r2s2 complex was thought to be an 8-like structure tucked inside C1q's collagenous ...
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Why did the protein structure prediction accuracy in terms of GDT-TS decrease from 2008 (CASP 8) to 2014 (CASP 11)?

I read on https://doi.org/10.1038/d41586-020-03348-4: Why did the protein structure prediction accuracy in terms of GDT-TS (Global Distance Test — Total Score) decrease from 2008 (CASP 8) to 2014 (...
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How does the order of the pairs of cross-links in DNA determine the arrangement of the amino acids?

Quoting Richard Feynman from Chapter 3 of his book Six Easy Pieces, when he talks about DNA: Attached to each sugar along the line, and linking the two chains together, are certain parts of cross-...
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Why do large, aromatic residues prefer beta-pleated sheets?

I read in many journals that amino acids with branched and large aromatic R-groups have higher beta pleated sheet propensities. However, none really go in depth into the significance or reasoning ...
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Measuring the protein content using UV Vis

The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
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What makes a protein structure discernible? [closed]

In Lehninger's Principles of Biochemistry, Pg. 116 states that "parts of proteins lack discernable structure." What exactly makes this protein not readable? Is it the complexity of the shape ...
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Which condition is most likely to cause a buildup of materials in the lysosome?

Stated below, I must answer a question related to lysosomes. I am unsure of the answer, and have explained my reasoning after the question. Lysosomes contain hydrolytic enzymes that derive from the ...
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What are the stretch of amino acids?

I found the words "stretch of amino acids" in a newspaper article. "This lipopeptide matches the stretch of amino acids in the spike protein of SARS-CoV-2 exactly." What is the &...
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Collagen, are fibrils arranged in overlapping fashion too just like tropocollagen?

Collagen molecules (tropocollagen) are interlinked into fibrils, with a banded structure showing the spaces ("lacunae") between the molecules. Do fibrils in turn also interlink in a similar ...
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Eukaryotic cell lysate-based protein expression efficiency

What is average efficiency of eukaryotic cell lysate-based protein expression systems in terms of (mg of protein expressed) / (mg of lysate) ?
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Questions about Cohesin - what does the ATPase domain do, and any suggested PDBs to look at?

I've been reading about cohesin lately, and I'm confused about the head subunit interactions. I've read a few papers, and also found this nice figure from wiki that demonstrates the crux of my ...
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What is the purpose of co-translational transport?

During intracellular proteins synthesis, all proteins are made by free ribosomes in the cytoplasm and some, but not all ribosomes (those which make membrane or secretory proteins) move to the ...
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How can Chronic myeloid Leukaemic drugs reduce the production of the Philadelphia genotype?

How can Chronic Myeloid Leukaemic drugs (Tyrosine kinase inhibitors, e.g. imatinib, etc.) that act by inhibiting bind of ATP to the active site of the BCR-ABL1 protein actually reduce the prevalence ...
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Does glycerol in E.coli culture media somehow inhibit the lac-operon?

I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces ...
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Proinsulin is an 84 residue polypeptide with six cysteines. How many different disulfide combinations are possible?

Generally cysteine residues form disulfide linkages - so how many combinations are possible out of (say) six residues. Also can cysteine form bonds with all the residues?
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Is in the process of making soy protein isolate all (or most) of the protein trypsin inhibitor removed?

Being lactose intolerant and going to the gym I looked for lactose free protein powder. Soy protein isolate seemed like a good option until I read something about the protein Trypsin Inhibitor (TI). ...
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Determine similarity in percentages between species A and B, A and C, and B and C

The chart above is a graphic that shows the amino acid sequence differences between different organisms for a protein keratin. The question I am required to answer begins as, "Keratin is made up ...
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Can any molecule become a hapten?

Hapten are small-molecules, that can only become immunogenic when conjugated with a carrier protein. I was wondering if all small-molecules can become haptens (eg. by synthetic conjugation). Given ...
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What is meant by [protein name]+/- (ie “Myod+” and “Myod-”)

I have read a paper where this notation for protein names is used: Myod+ and Myod- (or another example, Myog+, Myog-). What does this indicate? In the paper I'm reading, and some brief googling, it ...
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Do voltage-gated channels in a neuron use ATP

I have a question about action potentials in a neuron. Do voltage-gated sodium and potassium channels use ATP? I mean when they are closed or when they want to open the gate, do they use ATP?
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Who discovered DNase?

I was recently studying genetics in which DNase had a crucial role in proving DNA to be the genetic material and I tried to find who discovered DNase (like the discoverer of DNA) but in vain. Who ...
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What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to align structurally different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, does that means the ...
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Howthe body differentiate between foreign and native protein? How does it know when to create an immune response? [duplicate]

How the body differentiate between a foreign and a native protein? Suppose there is a bacteria, it has lot's protein on its membrane, with specific structures. How does our body know it's the foreign ...
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What's superposition and thread in RosettaCM?

I'm a beginner in structural biology. I had a question while reading a paper on RosettaCM. What does RosettaCM's superposition and thread mean? I googled it. As a result, the following results were ...
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PDB id to protein environment ph [closed]

How can one find the information of a protein environment ph from its PDB id? Can one assume the ph to be the same as its cellular location?
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Why are some protein sequences known but their 3D structure isn't?

Why are there some proteins that have a known amino acid sequence, but their 3D structure is not known? Wouldn't finding the former in a lab lead to the discovery of the latter? Please correct me if I ...
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Does my reasoning about the first emergence of proteins make any sense?

In order to make proteins, a cell uses ribosomes, which itself is a structure made out of proteins. The first ribosome couldn't have been created with the help of ribosomes though, as the ribosomes ...
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What is the best way to find which domains in a list of InterPro IDs are catalytic?

What is the best way to find which domains in a list of InterPro IDs are catalytic? (In this case, we are looking at human enzymes and their domains' InterPro IDs.) Thanks in advance! Setz
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What is a Protein contact map, and how do I read one?

Protein contact maps are symmetrical and look great, but how does one read one? I tried to underside the following source: 'Understanding contact patterns of protein structures from protein contact ...
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How can protein allergens be passed from mother to baby via breastmilk is proteins are broken down after ingestion?

All over the Internet new mothers are urged to avoid dairy products, a slew of vegetables and even beef if their child displays symptoms of reflux. In the case of dairy, for instance, it is said that ...
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How do anticholinesterase pesticides kill nematodes?

Compounds that inhibit the enzyme acetylcholinesterase are commonly used as pesticides. In animals with centralized respiratory systems controlled by the nervous system, poisoning with an ...
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How are proteins containing other elements encoded?

If I understand correctly, proteins are formed by associating each three-letter DNA sequence to a certain amino acid. Yet there seem to be proteins which contain elements such as copper, which isn't ...
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Is this basic gene diagram correctly labeled?

I keep seeing this gene diagram, and I am not sure how to interpret it. I don't know what this diagram is called or where it was first depicted, but in the second picture, I have labeled it with what ...

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