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

learn more… | top users | synonyms

2
votes
0answers
184 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 ...
2
votes
0answers
55 views

Are there examples of PTMs that add different chemical groups (and mass) to different amino acids?

I'm talking about this type of post-translational modifications. What I'm interested in is not whether some modifications can only occur on specific amino acids (that's clear), but if the nomenclature ...
1
vote
2answers
259 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?
1
vote
2answers
58 views

Conserved proteins are non immunogenic

I read that proteins that have been highly conserved are non-immunogenic. Why is it so ? What is the special thing that makes it non immunogenic(antibodies against them are hard to make) ?
1
vote
1answer
100 views

What type of mutation causes Progeria?

I'm doing my High School biology final on Progeria, and am wondering what type of mutation causes this disease. I know that the LMNA gene codes for the "prelamin A" protein, and that protein contains ...
1
vote
2answers
247 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. ...
1
vote
1answer
180 views

Which concentration of BSA is recommended for dynamic light scattering experiments?

What is the recommended concentration of BSA to be mixed with water so as to prepare a very dilute solution in order to clearly study the intensity-intensity correlation with single scattering ? I ...
1
vote
1answer
24 views

Staphylococcus AG structure?

I found this statement in my study materials in the section of Staphylococcus The AG structure: protein AG (species specific); polysaccharide AG (serotype specific). I know what is ...
1
vote
1answer
103 views

Codon alignment via Python? [closed]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process. So far.. I retrive pairs of orthologous DNA sequences from ...
1
vote
1answer
419 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?
1
vote
1answer
32 views

How to parse SCOP parseable files PDB residue identifiers?

I am trying to parse the SCOP parseable files, specifically dir.des.scop.txt ver 1.75. But, I have been facing problems with the PDB residue identifiers in the file. This is a tab limited file and the ...
1
vote
1answer
52 views

Topology of protein

The domain structure of protein Z, which is composed of 180 amino acids, is shown in the upper part of the figure below. Protein Z is palmitoylated at a cysteine residue (the third amino acid) ...
1
vote
1answer
112 views

What are the differences between HPRD and BIOGRID databases?

What are the differences between HPRD and BIOGRID protein-protein interactions databases? What are their purposes? Why do we need two different databases? How is data collected into each one? How ...
1
vote
1answer
43 views

Dimethyltryptamine binding site on Sigma 1 type opioid receptor?

I asked this question Dimethyltryptamine and Sigma 1-type opioid receptor interaction but it seems that I didn't express myself well. I was looking for the place on Sigma 1 type opioid receptor where ...
1
vote
1answer
65 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)?
1
vote
1answer
18 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 ...
1
vote
1answer
40 views

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

I am thinking what can cause the swelling of high protein diet of Whey proteins. Liver does breaks those proteins to branched chain amino acids (BCAA), which can cause this swelling. However, I am ...
1
vote
1answer
23 views

If a gene altered causes cancer and creates a protein for cancer can the new protein be isolated in some way?

In the above title question, can the protein thats altered not be isolated (to separate out from other proteins) somehow? Is there nothing that can bind to the specific cancer proteins that will not ...
1
vote
1answer
22 views

Vesicular and non vesicular transport

I have to classify them either as transported in vesicles or without vesicles. What I think - Non-vesicular 2.vesicular 3.vesicular 4.vesicular 5.non-vesicular 6.vesicular 7.vesicular ...
1
vote
1answer
31 views

Removing Sugars Bound to a Protein

I recently purchased some Maltose Binding Protein and as the name suggests this protein binds to maltose. The problem I have is the protein arrive with maltose bound. I know this through native mass ...
1
vote
1answer
41 views

Protein Structure Statistics [closed]

Could you show me references of any works you know of where, 1- they take all the known protein structure data (that is the coordinate data of all the proteins in PDB database lets say or elsewhere) ...
1
vote
1answer
118 views

How do proteins get into the blood stream?

So I'm asking this in reference to the injection of insulin, which is commonly done subcutaneously (in the hypodermis, a fatty part of skin). Now I know proteins usually get into the blood when ...
1
vote
1answer
49 views

Dimethyltryptamine and Sigma 1-type opioid receptor interaction

Where exactly do dimethyltryptamine and sigma 1-type opioid receptor interact? I read in this When the Endogenous Hallucinogenic Trace Amine N,N-Dimethyltryptamine Meets the Sigma-1 Receptor but it ...
1
vote
1answer
34 views

Enzymatic Protein Deglycosylation of TCL

I've done O- and N- linked enzymatic deglycosylation of purified and lyophilized proteins. Following some modifications to the manufacture's protocol, I had great results. I now want a student to ...
1
vote
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 ...
1
vote
1answer
94 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 ...
1
vote
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 ...
1
vote
0answers
19 views

Planar circular DNA and protein

I am trying to develop a planar (two dimensional) lattice based framework to simulate ring (circular) DNA and proteins. To verify my model, I need to simulate real DNA and proteins. The base idea for ...
1
vote
0answers
11 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 ...
1
vote
0answers
14 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?
1
vote
0answers
33 views

Ferredoxin synthesis pathways

I have been thinking about some alternative CO2 fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of ...
1
vote
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 ...
1
vote
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 ...
1
vote
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 ...
1
vote
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?
1
vote
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 ...
1
vote
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 ...
0
votes
2answers
405 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 ...
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 ...
0
votes
1answer
105 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 ...
0
votes
1answer
57 views

Length differences between physically interacting proteins

What can be said on the length differences between interacting proteins? Are they usually of similar sequence lengths or not at all?
0
votes
1answer
356 views
0
votes
1answer
141 views

Need of X or Y chromosome protein after meiosis

After meiosis each spermatid get either the X chromosome or the Y chromosome. I know that the 4 spermatids formed from 1 spermatogonia are connected by cytoplasm and so the proteins made by X or Y ...
0
votes
1answer
43 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 ...
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 ...
0
votes
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?
0
votes
0answers
9 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 ...
0
votes
0answers
13 views

What are conditions for a membrane to be settled ? (centrifugation)

The cell membranes have 60% of proteins and 40% of lipids. And we know that medium density of proteins is 1,2 g/cm3 and the medium density of lipids is 0.92 g/cm3. How can we calculate the medium ...
0
votes
0answers
24 views

What percentage of possible proteins has been tested by human brain evolution?

When the human human brain is discussed, I frequently hear an argument that goes like this "If there was a simple chemical solution for people to be smarter, nature would've already found it". I'm ...
0
votes
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.