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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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1answer
203 views

What difference do trans and cis configurations of amide groups bring to the polypeptide chain?

Hi I was just wondering whether there would be any difference to the structure of the polypeptide chain, or any changes to a proteins characteristics, if it has more amide groups with a cis or trans ...
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1answer
564 views

What happens to the enzymes produced by the digestive system?

Our digestive system produces a lot of enzymes and they help to catabolize the food, and after completing their work are they excreted out or as they are also made up of proteins are they catabolized ...
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1answer
335 views

About the formation of protein [closed]

There is a question in my textbook which asks: "What does the glucose produced from photosynthesis form?" However one of the answers said that glucose forms protein. But I'm quite sure that amino ...
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31 views

Cows milk protein transferability through breast milk

I understand that cow's milk protein(casein) transfers through breast milk via the mother's diet. I'm looking for the process as in what hormone does it bind to to allow this process in some women ...
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86 views

Degradation of PMSF in protein extract while dialysing - safe for feeding to animals?

I would like to use the protease inhibitor PMSF in enzyme isolation. The obtained enzyme diamine oxidase (or better the protein extract) is tested oral on dogs. According to Wikipedia, PMSF has a ...
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1answer
63 views

For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex?

I'm trying to figure this out. I cannot find any publications that go into good detail about the chemistry of PBP inhibition by β-lactam antibiotics. PBPs cross-link adjacent pentapeptides to form ...
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1answer
69 views

Subset of Protein Crystal Structures (from PDB)

Is there a well-accepted subset of the Protein Data Bank set of protein structures that: Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural ...
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9k views

Do all proteins start with methionine?

Start codon AUG also codes for methionine and without start codon translation does not happen. And even the ambiguous codon GUG codes for methionine when it is first. So does this mean that all ...
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1answer
531 views

Problems with SDS-PAGE, no separation - what could be the problem?

I work in a lab were we have a common stock of 30% Acrylamide, TEMED, TRIS-HCl (pH6.8 and pH 8.8.) and a 10% (w/v) SDS solution pH 7.2. We use the recipe for loading buffer (which we of course mix ...
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2answers
158 views

Can DNA sequencing of food provide quantitatively the fraction of protein from chicken vs soy?

There is some news about a report from Canada's CBC about fast-food chicken items containing as much as 50% soy protein, based on DNA testing. I won't do the report the service of linking to it ...
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1answer
628 views

What's the difference between physical (direct) and functional (indirect) protein interaction?

I read that the Protein-Protein interactions one can consider are generally of two types, namely physical and functional, but I cannot get the difference between the two. I was just thinking that if ...
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0answers
91 views

When can helices form coiled-coils?

The other day, my teacher suggested we find out whether a chain of the following amino acid sequence would be able to form a coiled-coil: N-KIAEVRAQYEDVANKVRLIVE-C ...
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1answer
139 views

FPLC based separation of serum proteins

I am working on a project which involves bio-marker discovery in neuro-developmental disorders. I have an akta-prime FPLC instrument in my lab but I do not know how to use it. According to theory, ...
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155 views

How to quantify the “stability” of a protein complex?

From experiment we've identified a subset of known mammalian protein complexes as interesting (approximately 50 CORUM complexes). We'd like to do an enrichment-style analysis to know more about them. ...
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2answers
930 views

How can I evaluate the hydrophobicity and/or surface charge of a protein?

How should I evaluate protein surfaces in terms of hydrophobicity and surface charge properties of the surface. Particularly I am looking to compare hydrophobic patches or surface charge between two ...
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1answer
65 views

Can proteins/peptides pass through the intestine?

I've heard somewhere said that : Stomach cells do not absorb anything larger than single amino acids. Is that wrong? How do biological toxins (peptides/proteins) from mushroom or bacteria like ...
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1answer
44 views

Computational engineering of protein binding pocket

I have an X-ray structure of an enzyme with reported activity to a small molecule. This activity is rather low since it is not the native substrate. I can run molecular modeling simulations (e.g. ...
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2answers
322 views

Are there any examples in nature of two polypeptides joining into a single, continuous, third polypeptide?

Are there any examples in nature of two polypeptides join into a single, continuous, third polypeptide like this: (Where all the indicated amino and carboxyl groups are on the main polypeptide ...
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2answers
481 views

Protein denaturation and edible toxins

As a protein denatured, it may lose its functions. So theoretically if I heat some type of biological toxins like poisonous mushroom to 100 oC or higher temperature, will I able to eat it? (I know ...
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1answer
2k views

Effect of 2,3-bisphophoglycerate (2,3-BPG) on haemoglobin

When 2,3-bisphophoglycerate (2,3-BPG) binds to haemoglobin, a higher partial pressure of oxygen is needed to bring about 50% saturation of with oxygen. What is the physiological significance of this ...
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3answers
554 views

Meaning of “cognate genes encode the basic biological functions of proteins”

In the introduction to a review article entitled “Interpreting the protein language using proteomics” the author uses the term ‘cognate genes’ in a manner which I do not understand: Whereas cognate ...
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2answers
85 views

Can a bacterium survive without GroEL protein?

In prokaryotes, GroEL protein (together with GroES) is required for protein folding. Question: Can a bacterium survive without GroEL protein?
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1answer
4k views

What is difference between High quality and low quality proteins [closed]

I have seen in news that some bodybuilder died of taking steroids; when I went through details I learned that "low quality proteins" contributed to their death. I have studied about linkages in ...
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673 views

How lymphocytes in lymphatic system get oxygen?

We know that the gas-transporting protein hemoglobin is absent from the lymphatic system. So, how does gas transportation takes place in lymphatic system? Is mere diffusion from surrounding blood ...
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4answers
4k views

Measuring protein concentration, Bradford vs. Nanodrop?

I know that the bradford assay is a very standard way of measuring protein concentration after e.g. a purification. However, in the lab that I work in now they normally only use nano drop at the 280nm ...
3
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1answer
428 views

Protein purification: Linear elutions or stepwise elution, using imidazole or pH gradient?

I now work in a lab with a protein and a pre-made purification protocol, were they purify a His-tagged protein using linear elution which then gives a steady increase in the imidazole concentration. ...
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0answers
23 views

What is the estimated number of variant surface glycoproteins that trypansomes can express?

In "Vaccination against trypanosomiasis" by Greca and Magez they assert that there are "innumerable" variant surface glycoproteins that the parasite can express. What does innumerable mean here? These ...
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1answer
525 views

Classifying Polypeptides (and/or Proteins)

Since polypeptides are a linear chain of twenty amino acids, each having a single letter abbreviation (e.g. Alanine = A). So can a polypeptide be represented as just the sequence (say: ADN for an ...
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142 views

Retrograde/anterorade transport; kinesin/dynein; COP1/COP2; Endoplasmic reticulum/Golgi

I am getting slightly confused with all of the terms above and was wondering if someone could see if I have got this right: I think transport from the ER to Golgi is almost always from the plus end ...
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0answers
134 views

What is/are the effect(s) of altering the Tris concentration on polyacrylamide gels?

Why do we use two different concentrations of Tris (i.e. 1.5M Tris in resolving gel and 1.0M Tris in stacking gel)? For the gel to run properly there needs to be a different pH, but that can be done ...
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2answers
135 views

What is protein folding and how is it relevant to disease?

I am trying to understand what is protein folding and how it could help cure some diseases. When reading articles about it, it looks like the goal is to find perfect folds for proteins because some ...
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1answer
1k views

Clarify pre-column pressure vs. system pressure vs. backpressure for prepacked columns used with the äkta purification system

Background: I am using the Äkta pure system for protein purification, with prepacked columns from GE-healthcare. Just to take one example, I use the HisTrap 5 mL column (IMAC: immobilized metal ...
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1answer
253 views

Transmembrane protein: does signal peptide always form a loop?

So I have read a few times that b. SP probably forms loop not arrow. Loop enters channel (translocon) in membrane. SP loop is probably what opens (gates) the channel on the cytoplasmic side. ...
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2answers
950 views

Do all polygenic traits involve epistasis?

Consider the following statement All polygenic traits involve epistasis. I think its true because polygenic traits involve several genes interacting together to result in a certain phenotype and ...
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1answer
331 views

Identity and similarity for Multiple Sequence Alignment (MSA) of proteins

I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am ...
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1answer
35 views

Why the total phosphorylation of certain neuronal proteins decrease during development?

Looking at the effects of RIM1a which is a protein involved in neurotransmitter release. Any ideas as to why its total phosphorylation decreases as the rats develop? Many thanks Image; https://i....
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0answers
63 views

Generating all possible conformations of an Intrinsically disordered protein

I want to simulate interaction between the bHLH-LZ domain of c-Myc encoded protein and a test ligand. Since the domain is intrinsically disordered, I want to generate all possible conformations of the ...
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700 views

Is the signal peptide always cleaved during protein synthesis in the ER?

My university supervisor said that the signal sequence is always cleaved, however my text book differs. What I gather from my text book (though it isn't very clearly stated so i'm not sure) is that: ...
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1answer
108 views

How would one go about identifying unknown cell cycle checkpoint proteins (i.e., cyclins)?

No this is not 'homework'. I'm a PhD student, and this was something brought up at the end of a journal club recently, and one of the PIs posed this question and told us to think about it. It sounds ...
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1answer
73 views

How to find mutations related to disease for a protein?

I have done research on the protein (CYP3A4). I have its function, purpose and diseases (breast cancer, prostate cancer, testicular cancer, lung cancer). I am however having trouble finding the ...
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0answers
57 views

Atomic Force Microscopy Imaging of Proteins

I was reading about various imaging techniques, and I came across Atomic Force Microscopy (AFM). It sounds very interesting, and it also sounds like it is capable of imaging proteins (Page 4) http://...
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1answer
89 views

Protein degeneration/excretion in cell

If I inject a dose of GFP or some other types of protein into a long-living human cell like brain neuron cell. Will these proteins being degenerated or excreted over time?
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10k views

Why is glycine considered a nonpolar amino acid but a polar molecule?

Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins? Also, is the backbone of a protein nonpolar?
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0answers
53 views

Do we understand how (some) proteins work? [closed]

Are there proteins whose operation we can describe from first principles using chemistry or physics? I've had introductory college courses in biology, and some classes in neuroscience, so I know that ...
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1answer
1k views

How do detergents interfere with protein assays?

This has been getting me stuck. I've tried to understand what a detergent would do in an assay, but I can't figure out whether it would affect the protein or the reagent (say, in a Bradford assay).
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0answers
23 views

Gene products of recessive/mutated alleles

I probably would not cite a specific example, but some recessive allele work by encoding for the non-functional form of an enzyme. While the dominant allele encodes for sufficient levels of functional ...
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1answer
42 views

Could all mammalian receptors be described as allosteric?

Allosteric regulation in enzymes is where a molecule binds at a site other than the active site and thus changes the tertiary structure of the active site, hence altering the binding of substrate and ...
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0answers
50 views

How do spiders get silk from their spinnerettes?

I'm 13 and writing a report on spiders. How do they use the silk protein gel from the spinnerets? How does it get from the spinnerets to the web? P.S. I know how silk is created, all the way up until ...
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2answers
538 views

Does heating proteins before a SDS-PAGE gel effect gel result?

I need to isolate a protein that a bacteria has excreted into an agar plate. My plan is cut out parts of the agar, heat the agar to melt it and then concentrate the protein through some purification ...
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1answer
6k views

What is the meaning of “E-value” in the BLAST search?

After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that? https://en.wikipedia.org/wiki/BLAST This expectation or expect value "E" (often ...