Questions tagged [proteins]

For questions about proteins. Proteins are biopolymers consisting primarily of polycondensated amino acids.

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38 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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2answers
3k 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 ...
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1answer
950 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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1answer
7k 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 ...
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2answers
71 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
260 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,...
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2answers
1k 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 ...
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1answer
365 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
586 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 ...
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2answers
3k 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 ...
2
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1answer
35 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 ...
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376 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
3k 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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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 ...
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38 views

Effect of protein hydrophobicity on metal interaction

I'm studying how metals and proteins interact (metal-protein complexes). I've found that almost all proteins could bind with metal at higher $\mathrm{pH}$ values, but also found some proteins showed ...
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54 views

Is there a model for (quality of) two-component-polymerization (dependent on e.g. concentration)?

Sadly my chemistry background is only from high school (I'm a roboticist), but I try my best to explain the problem: Situation: Lets say I have two water based solutions/suspensions. One contains ...
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123 views

Are there super(calorie-)dense foods?

It’s commonly reported that there are 9 kilocalories per gram of fat, 7 per gram of alcohol, and 4 per gram of carbohydrates or protein. But these figures (with the exception of that for alcohol, ...
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1answer
219 views

Why does this protein seem to have multiple chains?

I'm looking at the structure of this protein, which I beleive is supposed to be a single polypeptide chain, since on the PDB page it says: Unique protein chains: 1 But using the 3D viewer, there ...
5
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3answers
802 views

Why are protein hydrophobic cores denatured by heat when entropic forces should be favoured at high temperature

The hydrophobic interaction is thought to be driven by an entropic force. If it is, shouldn't hydrophobic interactions be stronger at higher temperatures, where states of higher entropy are favoured? ...
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3answers
2k views

Buffer Capacity Calculation

I know buffer capacity is the following: $$β=\frac{Δ(\ce{H+})}{Δ(\mathrm{pH})}$$ specifically the amount of acid/base that needs to be added to change pH by 1 unit. If I have data about how pH of a ...
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2answers
2k views

What happens when you mix milk and coke?

Add small amounts of milk to a bottle of coke, and you end up with a white-ish precipitate with a clear liquid on top. "The Internet" seems to agree that phosphoric acid in coke reacts with something ...
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0answers
771 views

Why do Bence-Jones proteins behave differently in urine heat test?

The preliminary test for proteinuria (proteins in urine) is precipitation/turbidity on heat due to denaturation. This turbidity should not disappear when 10% acetic acid is added - to differentiate ...
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1answer
1k views

Gel electrophoresis separates proteins on the basis of what property?

In SDS-PAGE for separation of proteins, SDS is an ionic detergent that coats the unfolded protein to mask its native charge and give at a uniform charge to length ratio. Since the length of the ...
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4answers
2k views

Does quantum mechanics play a role in protein folding?

Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. However, for the initial micro-steps of folding, when an atom, or a configuration of atoms, can ...
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1answer
295 views

Alternative to Hanging Drop Crystallization

Forgive my ignorance if I am way off, but I was having a look at the crystallization of a number of different substances (e.g. proteins) through the hanging drop vapour diffusion method. The examples ...
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1answer
217 views

What is the molecular mechanism behind oncotic pressure?

I can't wrap my head around the idea of oncotic pressure and osmolarity, logically. I imagine a blood vessel. It is filled with proteins, like a ton of proteins and solutes. So this means, according ...
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1answer
3k views

How can proteins reduce surface tension?

How can the protein lactalbumin reduce the surface tension of water and work like an emulsifying agent in milk?
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1answer
122 views

Effect of His-tag on enzyme activity

In my biochemistry laboratory class, I designed an experiment to study the effect of a His-tag on enzyme activity. First, I measured the activity of the His-tagged enzyme. Then, I cut off the His-tag (...
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1answer
141 views

Is the structure of a crystalized protein the native one?

When one finds the 3D structure of a protein by crystalizing it and then making a X-ray experiment, how does one know that the geometrical configuration of the crystal is the same (or even close) to ...
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2answers
2k views

Why are there no hydrogen atoms in the crystal structure of a biomolecule?

I am taking a physics and chemistry at the nanoscale class at my university and for a project I must learn how to use Visual Molecular Dynamics (VMD). One of the models involved in this project is apo-...
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0answers
112 views

RCSB PDB - how to choose between multiple copies of the same protein?

I want to map the location of missense mutations on a protein, SERPINB3. I intend to do this using PyMol and download the protein structure from RCSB PDB. However, ...
6
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1answer
433 views

Protein Data Bank: Asymmetric Anit/Biological Assembly

For a schoolproject I have to interpret the 3D structure of an imatinib-BCR ABLC kinase complex. When I visited the PDB website I downloaded the PDB file corresponding to this complex. Once I opened ...
2
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0answers
44 views

What are some technologies/biosensors for real time kinetic analysis of reactions? [closed]

I am in a lab that has used surface plasmon resonance (SPR) and ELISA very heavily over the past few years, and we are thinking of getting a new machine. I'm wondering what other technologies exist ...
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157 views

Energy required to break salt bridges in peptides and proteins

Is there a way to calculate the energy required to break a salt bridge in a peptide or on the exposed surface of a protein in aqueous solution? Is there any useful literature on this topic? I'm ...
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1answer
686 views

Turns in beta-alpha-beta loops (protein motifs)

In the context of protein secondary structure, do the loops between strand and helix in a beta-alpha-beta motif form into the conformation known as a beta turn?
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2answers
812 views

What is the difference between crystal structures of proteins, organic and inorganic materials?

From the definition of crystal and the main differences between crystalline and amorphous material, it is known that crystal formation requires ordered bonding between atoms or molecules. How can ...
4
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1answer
2k views

Mechanism of protein precipitation with TCA

In practice, TCA (trichloroacetic acid) is widely used for quantitative protein precipitation, but so far I have failed to discover the exact mechanism of TCA action. I highly doubt it's just the ...
23
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2answers
3k views

Why is the cyanide ion toxic?

As the title implies, what is the molecular basis of cyanide toxicity? I did some searching around at the CDC and it only states that it prevents cells from using oxygen. I also read how it could take ...
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1answer
683 views

why do we denature proteins before mass spectroscopy?

I'm learning about mass spectroscopy in particular the use of it in analyzing protein structure. they said we have to use trypsinolysis to cut the protein to segments, but why does the protein have to ...
3
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1answer
121 views

Why does no antitoxin for botulinum type H exist yet?

Antitoxins against the botulinum toxins type A–G produced by Clostridium botulinum are known. Why does none exist against the type H botulinum toxin yet?
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2k views

Why do unboiled eggs last longer than boiled eggs?

Just like the title says, I watched this video https://youtu.be/CHMY4G9gTPA and then became intrigued.
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1answer
3k views

Why does capping after each coupling in Solid phase peptide synthesis improve the results?

Why does capping after coupling improve results during solid phase peptide synthesis (SPPS)? The Case: I have conducted a lab experiment where we coupled three Fmoc-protected amino acids, and did a ...
4
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1answer
102 views

How to connect proteins via disulfide bonds computationally?

I want to connect proteins together to form a dimer. As seen in the picture, the monomers come close to each other along the edge of the higher-order structure (forget about the sulfate there). How ...
5
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1answer
89 views

Thermal stability of charged and uncharged alpha helices (the concept of alpha-helix capping)

I just learned that charged alpha helices are less thermally stable than uncharged ones. The only difference I see between them would be a larger dipole moment in the charged helix, but how would this ...
5
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1answer
381 views

Tandem mass spectrometry: a1 and immonium ions

In tandem mass spectrometry of proteins one will usually end up with a mix of $b$ and $y$ fragments but also $a$ fragments and immonium fragments. My problem is that wouldn't an $a_1$ ion be the exact ...
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1answer
88 views

Protein purification with Cobalt

Cobalt exhibits a more specific interaction with histidine tags, resulting in less nonspecific interaction than nickel. For this reason, cobalt is the preferred divalent cation for purifying His-...
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1answer
199 views

Hydrolysing large molecules to reveal amino acids

Consider Oxytocin: I am asked to hydrolyze Oxytocin and reveal 5 amino acids which are the result of this hydrolysis. I must admit I have no idea where to begin. I know that generally amino acids ...
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1answer
149 views

How does formylation of a nitrogen change the hydrophobicity of a target protein?

How does formylation, of the sort shown here: (from this Wikipedia page) affect the hydrophobicity of the target protein? Can we say anything general about adding a formyl group to a nitrogen?
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1answer
612 views

Is there a chemical test for gluten?

I am looking for a chemical test for the presence of gluten: however, having looked online for such a thing, all the results seem to be about 'home testing kits' (presumably for people with a gluten ...
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1answer
10k views

Can acidic conditions break disulfide bonds

I am denaturing a protein using organic solvent and acid (49:49:2% water:methanol:acetic acid), but I want to maintain the disulfide bonds. My chemistry knowledge isn't good but disulfides are broken ...