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

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127 views

What role does a protein's size have on protein-protein interactions?

Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
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0answers
39 views

Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?

E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms ...
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34 views

Functional modules in viruses

I am interested in protein function within viruses, especially on how they work together. Is there any study about grouping proteins in viruses as functional modules?
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1answer
107 views

DNA Replication

I just wanted to understand the basic steps behind the replication of the lagging strand of DNA: Have helicase unwind it first DNA Primase lays down RNA primers in fragments, called Okazaki ...
2
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1answer
71 views

How to bind antibodies to study their properties?

I want to experimentally look at the behavior of antibodies. To do so, I need to be able to bind these antibodies to a substrate. Does anybody know of a good substrate to use that antibodies bind to? ...
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2answers
69 views

What nutritious insects exist to farm that require the least attention?

What nutritious insects exist to farm that require the least attention? I'm looking to automate simply, in a self regulating way. Edit: To add detail, I imagine the insects would live densely in a ...
5
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2answers
354 views

Can proteins move outside cells?

I am trying to learn about basic cell biology, and have what is probably an extremely simple question. So this is how I understand it so far: Proteins are made from amino acids. This process is ...
9
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1answer
141 views

Protein data bank syntax: Can two protein secondary structures “overlap”?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
5
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2answers
256 views

What medical and commercial proteins are made using genetically modified animals?

Recombinant technologies in micro-organisms being used to produce commercial and medically useful proteins like insulin are fairly common. However some proteins are still produced commercially in ...
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31 views

Ovalbumin Detection

Is there a practical way to detect whether or not a baked good has egg in it? I'm thinking of something that can be brushed on to evolve a color change. Any help is appreciated.
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0answers
46 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 ...
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1answer
1k 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
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1answer
58 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?
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2answers
275 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. ...
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0answers
19 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
282 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 ...
3
votes
1answer
105 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 ...
2
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3answers
104 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 ...
2
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1answer
106 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 ...
0
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1answer
127 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
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1answer
54 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 ...
3
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1answer
93 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.
4
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1answer
1k 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 ...
3
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2answers
117 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 ...
5
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1answer
309 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 ...
6
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1answer
91 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 ...
4
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1answer
32 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?
6
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2answers
683 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 ...
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0answers
46 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?
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0answers
38 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 ...
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1answer
572 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?
3
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2answers
258 views

JMol “calculate HBONDS”: which atom is the donor/acceptor?

JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds. Here's one line from an example ...
6
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2answers
1k 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
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3answers
338 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 ...
12
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5answers
3k views

Can any protein be phosphorylated?

I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (Skowrya et al., 1997). I have heard of ...
17
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2answers
2k views

Do gene expression levels necessarily correspond to levels of protein activation?

I have seen a lot of research into molecular mechanisms of diseases/phenotypes use measures of RNA as a 'proxy' for the level of protein available in the cell. Is this actually valid? My problem ...
7
votes
1answer
179 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
242 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
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1answer
77 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. ...
13
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1answer
7k views

What effect has changing pH and salt concentration on protein complexes?

I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt ...
3
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1answer
258 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
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1answer
236 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 ...
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0answers
464 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
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1answer
48 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 ...
11
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1answer
1k 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
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2answers
246 views

How many human proteins are very well characterized?

Following up on How many human proteins have a solved 3D structure?,is there a list of very well characterized human proteins / protein complexes? My criteria for "very well characterized" ...
3
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2answers
92 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). ...
2
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0answers
193 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 ...
12
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4answers
203 views

Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?

What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them? If none are known, what computational tools might be used to search for such examples?
5
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1answer
199 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 ...