Polypeptide chains of amino acids folded into shape by charged R groups
0
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1answer
9 views
What proteins are transgenic mice used to produce?
I have heard of recombinant technologies being used to produce commercial and medically useful proteins like insulin. However, until recently, I was aware that transgenic animals are still used to ...
2
votes
0answers
13 views
How to use mechanical microstrainer to extract tissue proteins from human?
Background:
There are many methods to extract proteins form human tissues out there. The majority of them use an extraction buffer containing variable concentrations of detergents and protease ...
1
vote
1answer
29 views
How difficult is to renature a protein?
I know of Anfinsen's experiments and I'm aware that some denatured enzymes may regain their lost activity through the removal of the denaturant agent. What I'm unaware of is how rare is it for a ...
0
votes
1answer
27 views
SNPs mapping into protein
Starting a new project on protein-protein interactions and SNP analysis tool development. I would like to ask how does SNPs is mapped into protein? What does mapping means?
0
votes
0answers
22 views
CRISPR/Cas9 plasmid editing question [closed]
I would like to try to use the exciting new CRISPR/Cas9 system two make 2 ds breaks across about 1kb, then via homologous recombination introduce a much smaller selection marker. This done within the ...
0
votes
0answers
15 views
activate a drug using deoxycytidine kinase in vitro
I need to activate a drug similar to the way it is activated in the cell. My set of molecules called Nucleoside analog reverse-transcriptase inhibitors (NARTIs or NRTIs) need three phosphate groups to ...
2
votes
1answer
32 views
Using DTNP to find free thiol groups on a protein
I've been tasked with using DTNB to find the number of thiol groups on a molecule of Bovine Serum albumin (BSA).
After measuring the absorbance, finding the concentration of TNB and calculating the ...
2
votes
1answer
44 views
How long does a tan last?
How long do melanocytes and melanosomes continue to protect DNA after UV exposure? Basically, if skin is tanned, then over the next month it is shed, will melanocytes continue to produce high levels ...
1
vote
2answers
67 views
PEG-silane treatment: why incubate for 18 hours at 60 degrees Celsius?
I am conducting a biochemistry-related experiment and I have been unable to understand a step which is commonly performed.
My aim in this step is to apply a PEG (Polyethylene glycol) silane layer.
...
0
votes
1answer
44 views
Why does the PR form of phytochrome exist?
I know how it gets converted because PR is more stable and when there is neither red or far red light PFR naturally converts to PR. But what is the point of it? If PFR is the biologically active one ...
2
votes
1answer
41 views
PTMs of proteins via mass spec?
I understand that mass spec is widely used to study PTMs like glycosylation of proteins, but how can mass spec determine correct PTM structure of say glycosylation if two glycan structures have the ...
2
votes
3answers
45 views
What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
1
vote
0answers
19 views
What is the translation termination efficiency in mammalian cells?
When I express proteins in bacteria I put at least two stop codons at the end of the gene to increase the termination efficiency. Is this the case in eukaryotic cells too? If I put a single stop codon ...
2
votes
0answers
32 views
Where to put the gene after eukaryotic promoter for best expression levels?
As far as I know there is an optimum distance between a promoter and the gene for the best expression levels. What is that distance for common promoters like CMV, SV40? If you have a first hand ...
4
votes
2answers
67 views
Differences Between Protein Motifs and Protein Domains?
I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins. Any suggestions would be much obliged.
3
votes
1answer
55 views
205 nm UV-Vis readings
Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.
3
votes
1answer
95 views
What is immunopanning (vs. immunoprecipitation and FACS)?
I had never heard the term before today. From what I can tell, it's using antibodies to purify a cell population of interest. I would appreciate more details, especially in how it differs from ...
0
votes
2answers
35 views
More proteins from diet when common cold and flu?
My coach says that I need to eat 1.2 - 1.5 grams of proteins per kilogram when I have a common cold and flu.
I normally eat one gram of proteins per kilogram, while double it when doing my exercise ...
3
votes
2answers
53 views
High sequence similarity but start codon isn't methionine
I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(>80%) with known proteins. However, the start is not a methionine. Is ...
2
votes
1answer
22 views
Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?
I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently.
I've found a huge amount of extremely interesting papers about how biological network ...
5
votes
1answer
52 views
Solvent Accessibility, the 20% cut-off method
I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value.
I understand how the RSA is ...
1
vote
0answers
26 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 ...
6
votes
2answers
156 views
Why is absorbance at 280 nm for protein solution going up when I measure repeatedly?
I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with ...
4
votes
1answer
83 views
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 ...
0
votes
0answers
42 views
Why aren't D-amino acids used in proteins? [duplicate]
Possible Duplicate:
Why are amino acids in biology homochiral?
Why are only L-amino acids used in protein construction, and not D-amino acids?
2
votes
0answers
25 views
Endocannabinoid Transporters - which ones are Likely to Exist and what is the Evidence for their Respective Existence?
Endocananbinoid = Endogenous Cannabinoid or CB1 and CB2 ligands.
I'm asking which endocannabinoid transporters exist and could the one answering show all the evidence for the existence of the ...
4
votes
1answer
25 views
position of cell penetrating peptide
I'd like to add a cell penetrating peptide to my custom peptide (30aa). Can I just add it to the end of the peptide sequence or does it have to be positioned on an outward facing external chain?
1
vote
1answer
44 views
What is the difference between average and monoisotopic mass calculations of peptides?
I often have to calculate the mass of peptide sequences using calculators such as here.
I have the option of calculating the average and monoisotopic mass, but what is the difference?
0
votes
0answers
42 views
Bradford Protein Assay [closed]
Please would somebody help me to solve the following exercise:
Determine the protein concentrations of the four unknown samples (A,B,C,D) using the raw data obtained from a Bradford assay.
...
6
votes
1answer
75 views
Proteins that are strongly overproduced in E. coli and S. cerevisiae?
I'm looking for some pointers to proteins that produce at really gigantic levels in E. coli and yeast (S. cerevisiae). Can anyone point to some champion proteins?
Even in inclusion bodies and non ...
3
votes
1answer
55 views
High protein turnover rate and protease inhibitors?
I work with mice, and I want to see what happens to some specific proteins in the mouse brain after IL-1b injection (intracerebroventricular).
I have a problem: when I measure the mRNA and protein ...
6
votes
2answers
165 views
Gene & Protein nomenclature: N-Myc, c-Myc, et. al
Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins?
I think I know that for genes, we use an italic ...
3
votes
3answers
125 views
What is a good list of unsolved protein structures?
I'm trying to get a list of unique soluble structured proteins that don't have a solved structure. That is, they aren't the usual membrane proteins or some derivative of another protein.
Things that ...
5
votes
1answer
67 views
Recombinant protein fraction in E. coli
If a protein is heterologously expressed in E. coli under the T7 promoter, what fraction of the total protein concentration in the cell is the heterologously expressed protein? What could be its ...
6
votes
1answer
94 views
Determining if a specific proline is cis or trans in the protein?
While peptide bonds usually adopt the trans conformation, peptide bonds to proline can exist in either cis or trans conformation. The isomerization between cis and trans is slow, and has been shown to ...
2
votes
1answer
46 views
Why glycoproteins are better than non-glycoproteins in fulfilling biological tasks?
I have just an intuition that the carbohydrate part of glycoproteins help them to fulfil those tasks like in plasma membranes.
You can also get many more receptors if you can use carbohydrates too.
...
0
votes
0answers
61 views
What happens to proteins when they absorb UV? [closed]
I know that proteins strongly absorb UV at 280 nm.
I have 3 questions:
What happens to proteins when they absorb UV?
Do different proteins absorb different wavelengths ?
Does water absorb UV as ...
3
votes
1answer
149 views
Ammonium sulphate precipitation assay pH dependence
In general does the pH effect the precipitation, e.g. would a pH of 6 cause less precipitation than pH 7.5. Or are they unrelated?
4
votes
1answer
114 views
If proteins have an overall charge, how do membrane proteins traverse through the hydrophobic region of the plasma membrane?
These two concepts seem almost contradictory, proteins have a net negative charge due to the amino acids in them each having a small negative charge, yet membrane proteins are able to exist traversing ...
0
votes
0answers
98 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 ...
2
votes
1answer
42 views
Preserved alpha complementation over evolutionary time?
Has the result of alpha-complementation ever happened via mutation through evolutionary time, and been preserved in modern day organisms?
In other words, has a functional gene product ever been split ...
2
votes
0answers
152 views
What specifically allows alpha-complementation in beta-galactosidase?
I'm familiar with the use of alpha-complementation of beta-galactosidase with the pUC alpha-peptide and the M15 lacZ gene product, and would like to hypothetically apply alpha-complementation in other ...
3
votes
2answers
79 views
Have proteins been observed to come into existence through mutations and natural selection?
What is an example of a functional protein that has been observed (in real time) to have come into existence through mutations and natural selection (not through an existing one being made defective). ...
4
votes
1answer
125 views
How are DNA polymerase error rates measured?
It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
7
votes
0answers
193 views
Rosetta ab initio prediction and protein-protein interaction fitness help
I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to ...
5
votes
1answer
88 views
Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?
I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as ...
0
votes
0answers
84 views
which free videos with 3d animations simulating protein processes are there? [closed]
I have found a group that creates free videos that show life within (or outside) a cell as it really is, at the near molecular level. They use real protein structures with in-molecule dynamics ...
4
votes
1answer
60 views
Determining if a Protein Model Contains a Backbone Clash
I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be ...
11
votes
1answer
380 views
Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?
I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express.
Depending on the ...
7
votes
2answers
72 views
Exactly which amino acids are phosphorylated in higher plants during state transitions?
I know it is usually stated as the threonine residue near the N-terminus of either light harvesting complex (lhc) b1 or lhcb2, but if this is somehow lost, say in a mutant, is the system flexible ...
