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 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 ...
4
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1answer
58 views

What is the advantage of the way eukaryotes initiate translation?

The eukaryote and prokaryote mechanism for translation is slightly different. Is there any advantage of the eukaryote translation mechanism ? Edit : I specifically want to know why eukaryotic ...
4
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2answers
89 views

Why don't amino acids get linked in the functional groups of acidic and basic amino acids?

There are 'acidic' and 'basic' amino acids like aspartate and histidine. When protein is synthesized with those amino acids, what ensures that the to-be-assembled amino acids will not bond to the ...
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0answers
23 views

Where exactly is NMDA Glutamate, Glycine, Allosteric and Channel blocker location?

I am reading about NMDA. I ran a active site location finder on NMDA1 which is Uniprot Q05586.1 and it said the highest quality binding site was near residues ANYSIM. However there are so many options ...
3
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1answer
91 views

Superposing DNA

I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...
1
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1answer
70 views

Which is the correct statement on proteins?

I need help with one of the questions on my biochemistry assignment Choose the correct statement on proteins: a) proteins are folded by alpha-helix b) proteins can preserve their function even if ...
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0answers
12 views

histamine inter-cellular and cytoplasmic binding site

I noticed that HRH (histamine receptor) has an inter-cellular and cytoplasmic binding site of anti-histamines which are equal in binding energy. Does anyone know what is the function of the well ...
2
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1answer
39 views

How do you differentiate between SR protein and SR-like protein?

What are the criteria that the researchers use to choose whether a protein is an SR protein or and SR-like protein?
0
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1answer
42 views

Function of ER in reviewing mutated proteins

At least in the case of Cystic Fibrosis it happens that a mutant protein (which could actually function!) is held in the ER because the ER detects it as misfolded. Does this happen in every type of ...
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1answer
57 views

Is there any definition of complexity about gene and protein according their function?

Sorry for such a question,if it is too naive. Is there any definition of complexity about gene and protein according their function?If so,what is the relation between them?
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1answer
64 views

What are the characteristics of a promising drug target?

When researchers are looking to start developing a drug, what characteristics do they look for in the potential proteins (assuming they already have good quality structural models)?
3
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2answers
39 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 ...
2
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1answer
32 views

Material on the analysis of (micro)array data

I'm at the moment analyzing cytokine array data. The available material on the statistical analysis of these data is more than unsatisfactory. Since a lot of effort is being made in the analysis of ...
5
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2answers
76 views

Are SLC52A2 and GPR172A really the same?

The official HUGO gene nomenclature page says that GPR172A (Gamma-hydroxybutyrate receptor) and SLC52A2 (riboflavin transporter, member 2) are the same. The sequence reported by Andriamampandry seems ...
2
votes
3answers
99 views

What do cells do when they aren't creating proteins?

I've always thought that the majority of the "work" in a cell is protein production, until I read the following. The Wikipedia article on the central dogma of molecular biology states this: 80% ...
0
votes
1answer
103 views

Why not produce protein based on condensation reaction?

I'm fairly new learning about protein. As I know protein can be synthesis by condensation reaction. And the current method to produce protein is purify them from an organism. So why not produce ...
9
votes
2answers
120 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
38 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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0answers
31 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
92 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
votes
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? ...
4
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0answers
34 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 ...
0
votes
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
votes
2answers
298 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
134 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
239 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 ...
0
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0answers
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.
2
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0answers
44 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
55 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
243 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
231 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
92 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
votes
3answers
94 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
92 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
103 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
51 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
votes
1answer
88 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
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
112 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
votes
1answer
253 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
votes
1answer
88 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 ...
1
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0answers
78 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 ...
4
votes
1answer
29 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
634 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
3k 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
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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?
2
votes
0answers
37 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 ...
1
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1answer
406 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?