Questions tagged [proteins]
For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.
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23 views
How to remove protein smell?
When I took a chemistry class a few years ago and I remember the teacher saying , like dissolves like. So with that logic, is there a say to denaturalize protein? I spilled a protein shake in the back ...
5
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1answer
64 views
Can =NH2+ in Arginine's side chain form hydrogen bonding at physiological pH?
I know that at physiological pH, Arginine will have its $\ce{=NH}$ protonated to $\ce{=NH2+}$. I was wondering if this $\ce{=NH2+}$ can still form a hydrogen bond by being a donor? And does the ...
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0answers
20 views
Molecular dynamics after modeling a protein loop. Necessary?
Firstly, I am postign this question to both chemistry and physics stacks exchange as I am not sure to which it belongs and to use the benefits from both sites.
I have modeled missing loops in a PDB ...
1
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0answers
28 views
cluster of milk [closed]
I have a problem with milk when we are making yogurt in factory. When the milk pass through the machine it clogs the filter of the machine because the cluster that formed on the filter. My question is ...
4
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1answer
219 views
Is chitin actually protein?
Recently insects are featured as a protein rich source for human nutrition. That humans can really digest chitin through chitinase enzym has been only recently confirmed.
But, does the chitin shell ...
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0answers
72 views
Parallel reactions with for and reverse reaction
I am working on protein folding-unfolding kinetics and recently we have encountered a problem with fitting the data because we are lacking the analytical equation describing our model.
We have a ...
0
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0answers
46 views
How does sodium hydroxide dissolve flesh? [duplicate]
How does sodium hydroxide or bases dissolve flesh? I want to know mechanisms how sodium hydroxide dissolves our body protein.(or other organnic matters)
Thank you in advance.
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0answers
76 views
Normal Mode Analysis in Amber
I'm working on a project in which I would like to perform Normal Mode Analysis to explore conformations of a small protein. There are various tools out there to do this, but I would also like to ...
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1answer
46 views
Why Greek yogurt has higher protein concentration?
During fermentation, no nitrogen is added and the number of amino acid molecules cannot increase. Why does it have a higher protein concentration than milk?
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1answer
151 views
Formating chemical equations for proteins binding in hugely complex configurations
In a previous question I asked about a simple case, I'm now trying to write equations for proteins that bind multivalently. In the simplest case proteins $A_1$ and $A_2$ can bind to up to two $L$ ...
3
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2answers
33 views
Why does the isoelectric range decrease as an Alanine chain grows longer?
The pK1 and 2 values for alanine are 2.3 and 9.7. In the dipeptide Ala-Ala, they are 3.1 and 8.3 and in tri-peptide Ala-Ala-Ala, they are 3.3 and 8.0. Why does this trend in pKa values exist? Why does ...
8
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1answer
281 views
How to dock aggregated structures comprised of “elementary” protein units like LEGO pieces?
There are proteins with intrinsic symmetries. For example:
I was wondering how to use transformations such as: rotations, translation, replications to construct possible structures using 2 types of ...
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1answer
66 views
How to unify all the subunits in a PDB file?
A PDB may contain a TER token. For example, hemoglobin has 4 subunits separated by a TER identifier.
If we take hemoglobin's ...
6
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1answer
138 views
How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do ...
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1answer
152 views
How to visualize a crystal from a unit cell PDB and how to draw the unit cell's axes? [closed]
I am looking at the following PDB experimental data:
Length (Å) Angle (°)
a = 155.72 α = 90.00
b = 155.72 β = 90.00
c = 106.16 γ = 120.00
I find it hard to ...
6
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1answer
73 views
Biomolecular energy functions and entropy
From what I've been reading, it seems that entropy (rather than enthalpy) is the biggest driver of protein folding (especially the burying of hydrophobic residues). However, popular energy functions ...
3
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1answer
2k views
What happens to the t-butyl cation in the TFA deprotection of a t-butyl ester?
I am a first-year chemistry graduate student and I am currently learning how to synthesize proteins. I have reached a stage in the process where I need to deprotect a carboxylic acid moiety protected ...
2
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0answers
76 views
Calcium concentration in NMDARs e Nitric Oxide Synthase
My question is related to calcium $\ce{Ca^{2+}}$ concentration in NMDA receptors and nitric oxide synthase. I've found a very simple model that describes how the time change of calcium can be related ...
2
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1answer
297 views
What is the difference in the effect of DTT (Dithiotreitol) and SDS (sodium dodecyl sulfate) for PAGE?
In class, we have studied that when running a polyacrylamide gel with our protein sample to separate the proteins by molecular size, we can use several techniques, among which we have denaturing PAGE ...
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1answer
66 views
How to read these graphs and what are they called?
How does one interpret/read the following graph (found here) as well as on wikipedia or
What are these called?
3
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0answers
53 views
Formating chemical equations for proteins binding in multiple configurations
I am working on problems involving protein-protein binding, particularly ones in which two proteins may bind in two or more configurations, and where some of the resultant structures may also bind ...
4
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1answer
264 views
Mono-oxidized and dioxidized tryptophan
I'm translating a Russian text in which there is the following diagram of tryptophan degradation:
Further on in the text, hydroxytryptophan is called "the mono-oxidized form" (моноокисленная ...
8
votes
2answers
397 views
Why aren't chaperones considered to be catalysts?
I'm reading about protein folding on Wikipedia and I stumbled on a bit about a class of proteins called chaperones that aid in the folding of proteins by:
...reducing possible unwanted aggregations ...
15
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1answer
1k views
What is the nature of the Fe–O2 binding in oxymyoglobin and oxyhemoglobin?
Deoxymyoglobin ($\ce{Mb}$) is known to have iron in the +2 oxidation state; I believe this was deduced from its magnetic moment, which corresponds to four unpaired electrons in high-spin $\mathrm{d^6}$...
0
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1answer
518 views
Is protein folding thermodynamically favourable? If yes.. why? [duplicate]
The second law of thermodynamics dictates that the sum of entropy of the universe is always increasing. Is the process of protein folding a spontaneous process which is increasing the entropy? Is this ...
4
votes
1answer
157 views
How to measure a distance along the surface of a protein in a PDB
I would like to measure the distance between two active sites in a protein complex (pdb), but I do not find a straightforward way to do it.
To be more precise I need the distance along the surface ...
4
votes
1answer
464 views
Using baking soda paste (alkaline) to “neutralize” honeybee venom (acidic). Is this scientifically sound?
I recall reading (courtesy: my 9th grade Chemistry text-book, chapter Acids, Bases and Salts), something along the lines of:
Bee venom is acidic. This is why the area of skin (stung by a bee) is ...
2
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2answers
128 views
Why is the E2 protein important for protein degradation?
In the ubiquitination process, the E2 protein transfers ubiquitin from E1 to E3. Why can't E1 work with E3 directly to tag some protein with ubiquitin? Going further, why can't one of the E(1-3) ...
3
votes
1answer
93 views
Positive charge on a zwitter ion at pH=7?
I faced this question. But I am having some problems understanding the solution to this:
How can the negative charge on the peptide vanish on $\pu{pH = 7}$? Suppose, we have some $\ce{H+}$ donor on ...
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0answers
144 views
Hydrolysis of silk protein
I want to know how you would break down silk proteins into amino acids/peptides, and the end product be almost purely the silk or at least nontoxic for consumption/topical use (dehydrated into a ...
4
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0answers
82 views
How to make a sephadex slurry
I want to purify crude alpha-amylase with column chromatography. I am using a spehadex 75, But for some reason I can't find any information on how to make the slurry.
I can quickly find tons of ...
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1answer
63 views
Collagen: similarity of human to fish and meat amino acids [closed]
I am looking for a collagen supplement for my partner who has joint pain, bone pain, fatigue associated with ligaments, flaccid skin problems, and is just over 40. As she does not eat fish or meat, ...
2
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0answers
330 views
proteolysis - how to determine the partial or completeness of the cleavage reaction?
Though the question is about biomolecules, we agree the underlying functions, formation, degradation etc come down to chemistry, (then physics and maths). I am posting it here to receive an ...
2
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0answers
71 views
Do proteins have a smell?
Proteins are heavy and not so volatile. Does it mean that pure proteins do not have a smell?
7
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3answers
586 views
Is it known for sure that bases feel slippery because of the production of soap/surfactant?
Discussion around the question Why does bleach feel slippery? has started me thinking about the saponification explanation for the slippery feeling of basic solutions.
According to Wikipedia:
...
3
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0answers
33 views
Antiprion effectiveness of phenol
I am investigating ways to reliably decontaminate instrumentation that has come into contact with mammalian prions. Chaotropic salts and extreme pH are good at inactivating prions by disaggregating ...
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0answers
1k views
Terminology: what's the difference between “monomer” and “protomer”?
Using definitions from Wikipedia, a protomer is defined as "the structural unit of an oligomeric protein. It is the smallest unit composed of at least two different protein chains that form a larger ...
5
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1answer
600 views
Using electronegativity and atomic size to compare acidity of cysteine with serine
In proteins, the alcohol group of serine is generally more difficult to deprotonate than the thiol group of cysteine.
Serine and cysteine respectively:
In the literature, the explanation given is ...
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0answers
453 views
Why does viscosity increase upon the denaturation of a protein?
Measuring viscosity is one technique to monitor the tertiary structure of a protein. Why though? Why does viscosity generally increase when a protein is denatured?
3
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1answer
3k views
Why is % yield in a purification table measured using activity instead of total protein?
I'm trying to understand why % yield is measured with activity instead of total protein in mg. According to my biochemistry notes, activity is "1.0 units of enzyme activity = 1.0 μmol of substrate ...
0
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2answers
50 views
Is there a pH at which all proteins are negatively charged? How can it be determined?
I know that depending on the amino-acid-composition of the peptide the distance to the isoelectric point determines the charge. Is there a universal point at which all proteins are definitely ...
2
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1answer
167 views
How can absolute binding free energies be calculated?
In the calculation of binding free energies, such as between a protein and a ligand, I learned that absolute values cannot be obtained from simulation (such as taught in this lecture, slide 2). Rather,...
11
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2answers
985 views
Why do the physical properties of an egg shell change when the egg shell is exposed to vinegar for a week?
When an egg is kept in vinegar for one week, its hard calcium carbonate shell changes into a soft rubbery membrane. As vinegar is weak acetic acid, how does vinegar change calcium carbonate into a ...
0
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1answer
261 views
The definition of peptide, peptide bond and protein
According to what I understand the difference between peptide and peptide bond is that peptide is two or more amino acids (up to 19 -inc.) which linked together, while the term "peptide bond" refers ...
3
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1answer
237 views
Which is more stable chemically: DNA or peptide
Assuming enzyme-free environment, and the DNA and peptide are lyophillized, and then stored in vials under the same conditions (temperature and humidity).
On average, which would be more chemically ...
16
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2answers
2k views
What makes heat resistant proteins heat resistant?
We were doing the chapter Biomolecules in class the other day, and a doubt popped up once we reached the section on proteins.
We were taught that the stuff that keeps proteins together are: Ionic ...
3
votes
1answer
34 views
What aspects of a macromolecule/protein do the various contributions to its entropy relate to?
I've come across a few different contributions to entropy in macromolecules such as proteins: configurational, conformational and vibrational. The problem is that I can't seem to find a consistent ...
3
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0answers
320 views
NAMD free energy calculations (FEP, Alchemical)
I am trying to calculate the absolute free energy of a protein-ligand-complex using the free energy perturbation theory.
Following the alchemical route in this tutorial, I have calculated eight MD-...
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2answers
2k views
Why do amino acids hydrogen bond rather than ionic bond when they are forming secondary structures in proteins?
When peptide bonds are formed between amino acids, electron delocalisation causes the N to be more positive and the O to be more negative. As a result, why does 'hydrogen bonding' occur to form ...
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2answers
491 views
Where on the backbone does a peptide get protonated at low pH?
As a particular example, how does the backbone of a peptide look at $\mathrm{pH}~2$? Where does the backbone get protonated in such an acidic solution?
I know that at low $\mathrm{pH}$ the free ...
