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

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Influence of temperature on protein binding and decay rates

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions. Question In particular, my ...
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9 views

How does temperature influences rate of protein decay?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions. Question In particular, my ...
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0answers
9 views

VMD set molecule as top using script

I have 10 molecules in VMD main screen and I was wondering if there is a script command to change what molecule is the top. For example, molecule ...
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47 views

Influence of temperature on transcription, protein binding and decay rates

I am the kind of biologist who doesn't know much about molecular genetics and about the dynamic of biochemical reactions. Question My question concerns the influence of temperature on the dynamic of ...
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49 views

Is there a difference between any of these terms for proteins: “crystal structure,” “NMR structure,” “solution structure,” and “complex structure”?

My homework wants me to plot all crystal structures determined per year, but when I search on PDB for all structures, many of the articles say "crystal structure," but some say "solution structure" or ...
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17 views

can a bacterial protease inhibitor cocktail be used for Western Blotting involving HUVEC cells and HT-29 adenocarcinoma cells?

Dear fellow biochemists, I need some advice on Western Blotting, more specifically the use of certain protease inhibitors with the RIPA cell lysis buffer and protease inhibitor cocktail. A Millipore ...
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22 views

Deduce length order of 4 decapeptides based on the Ramachandran plot

I have stumbled upon the following past exam question: 4 decapeptides A, B, C, D, made only of glycine residues, have different conformations, and the phi and psi angles of individual peptides ...
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49 views

Pectinase Enzyme Assay

I am working on pectinase enzyme assay. I incubated 900 ul of substrate for 10 minutes in the water bath, followed by adding 2ml of DNSA reagent, then 100ul of enzyme extract added finally i read the ...
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37 views

What regulates the timing of the motion of molecular machines during DNA Replication?

This question is about this video I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines. I know that those big ...
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32 views

What is the biding site code recognized by the parts of the spliceosome

Another question about another Youtube video. At 0:50, the splicing process begins to remove the non-coding section of the DNA (intron), so the different parts of the spliceosome attach to the borders ...
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74 views

How to remove bad lanes in ImageJ Westernblot analysis

I use ImageJ to do an analysis of a Westernblot Image. If everything goes as wanted the workflow is fine. But if I do something wrong creating a lane there is no undo for a lane and also no way to ...
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What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?

I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an ...
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186 views

What can cause the bloating in high protein diet of Whey proteins?

I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins. Liver does breaks those proteins to branched chain amino acids (BCAA), ...
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488 views

Difference between Condensin and Cohesin proteins?

The chromosomal DNA is stacked with help of cohesin and condensin protein in which particular manner? Can cohesin be said to form kinetochore? How would they vary exactly? The terms are so narrowly ...
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3answers
99 views

More entropy: Atom or Macromolecule? [closed]

A question that appeared on my last exam was : Which of the following has greater entropy A) An atom B) A macromolecule The question doesn't specify anything else(i.e. type/size of atom or ...
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1answer
57 views

What I can do in order to improve the folding of the protein?

I am struggling with the expression of the certain protein. It seems that it is not properly folded and thus, it is not active. I tried to express it at the lower temperature and for the longer time, ...
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1answer
53 views

How to recognize a conserved motifs of the protein

I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids ...
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2answers
68 views

Turning publicly available genome data into proteins

I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller ...
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47 views

To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)

I have to answer a question about a sub-task of my thesis: Can the bacteria X produce the protein Y? I searched of course Google and BLAST. There is no data supporting that this specific bacteria ...
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21 views

Formation of peptide bond..?

Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by ...
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20 views

Can a protein be present in a protein-based complex but not important for the function of the complex

Suppose protein A is present in a protein complex ABC. Is it possible that protein A is actually is not important for the function of protein complex ABC? Or put alternatively, can a protein X not ...
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1answer
14 views

What does the term 'modified residue position' in phosphorylation mean?

Does it mean the position of the amino acid in the protein sequence, or something else? For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the ...
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4answers
78 views

Which point mutations in proteins are OK, and which cause significant change?

I heard that some point mutations in proteins are OK, like from alanine to glycine (I'm not sure, it's just an example), some will change the protein significantly. I want to understand deeper but ...
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68 views

What Proteins Are Universal To All Life Forms?

According to National Geographic, there are 23 proteins that are common to all life forms: All species in all three domains share 23 universal proteins, though the proteins' DNA ...
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169 views

Protein structures given in PDB and SNP's

There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB ...
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128 views

Why digest proteins into peptides for Liquid Chromatography - Mass Spectrometry?

Digesting (trypsin or whatever other proteolytic enzyme) proteins generates multiple peptides so the degree of complexity of the sample, at the peptide level, increases a lot. In addition there is ...
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54 views

level of organisation of proteins

Is there any disulphide bond in a quaternary structured protein? If yes, please provide examples. In tertiary structured proteins, what is(are) the most important characteristic(s) of tertiary ...
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82 views

alpha tubulin molecular weight problem

Is there any academic reference that shows α-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.
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What are the naming conventions for mutations of proteins?

I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50. Please can someone explain the ...
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108 views

What happen's to a virus's capsid after it injects its genetic material into the host cell?

After a virus (one of the varieties which infects the cell via injection and not endocytosis) injects its genetic material into the host cell, what happens to its protein coat? I would guess that it ...
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289 views

How are proteins formed?

Somewhere, I have read that we need to consume proteins to make amino acids to make new proteins. What does it suggest? How do we make proteins from proteins?
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27 views

How are cyclic hormones characterized?

I have a question regarding the description of a subset of peptide hormones, called cyclic hormones. Two examples of cyclic hormones would be somatostatin and melanin-concentrating hormones. I know ...
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1answer
36 views

What do the Clustal Alignment Symbols Mean?

Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?
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53 views

Selective Androgen Receptor Agonist

I'm looking for an inducer that strongly activates the androgen receptor, but not the glucocorticoid receptor that is not DEA regulated. I know that SARMS (Selective Androgen Receptor Modulators) are ...
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28 views

The use of proteins in memory creation

I have very limited knowledge of how the human memory works as I think, at this time, most people do. However, I have been reading and some articles which say, and I quote the article just linked ...
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84 views

Color van der waals bonds in swiss PdbViewer

I'm trying to color certain amino acid's van der waals bonds as in the following picture: can anybody please describe the steps to accomplish that?
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213 views

Are Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70 positively charged or negatively charged? [closed]

Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70,are they positively charged or negatively charged ? And which other solvents can be used as a substitute to water for preparing solutions in each ...
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1answer
114 views

How to wash the column during protein purification with GST tag?

I have been working with GST tagged proteins for the last 4 years and after loading the cell lysate into the column I was washing it with 20-30 column volumes of PBS and sometimes my proteins were ...
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28 views

Evolutionary rationale behind migration proteins

Tumor cells are able to migrate due to specific migration proteins. What is their evolutionary origin? Or are they simply deregulated?
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30 views

Protein Conformation Modeling

I'm interested in learning about computational modeling in biophysics. I have heard some amount about people modeling proteins as a network of ideal springs to examine things like conformation ...
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50 views

Curious about Brazzein

What is in compound "Brazzein" that it makes it 2000 times more sweeter than sugar? Can anyone please explain the science behind it?
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Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
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2answers
131 views

What are the functions of disulphide bonds?

What are the functions of disulphide bonds between amino acids in proteins or peptides?
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38 views

conservation of C-peptide sequence in the guinea pig

Where can I compare the C-peptide sequence of guinea pig with human or mouse? I am also interested in finding whether the guinea pig has insulin 1 and 2 to know whether I could use an anti-C-peptide 1 ...
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1answer
79 views

What is optical density in Lowry's protein estimation method?

I have a few questions: What is an OD value? Why do we use blank solution in Lowry's protein estimation method? If The OD of a protein is 0.01, what does it mean? Thanks in advance.
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To decrease the amount of proteins in the lymphatic drainage for short term

I am looking for some mechanism which can decrease the amount of proteins in the lymphatic drainage only for short term. Assume there is no flow between capillaries and lymphatic system because the ...
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23 views

What is the distribution of agent on plasma proteins in ECF?

I am studying Montelukast here: Montelukast is more than 99% bound to plasma proteins. The steady state volume of distribution of montelukast averages 8 to 11 liters. Studies in rats with ...
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25 views

fibrinogens and fibrins - are they the same molecule?

Some proteins are "activated", like fibrinogens; they are turned into fibrins by thrombins, and then the fibrins can aid in blood clotting. Are fibrinogens and fibrins the same molecule, just in ...
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873 views

Is there a protein in the eye that gets kinked by photons and shipped down to the liver to get un-kinked?

My friend made the claim that there exists a protein in your eye responsible for vision. This protein is sensitive to different wavelengths of light, and when it gets hit by the right wavelength, it ...