Questions tagged [proteins]

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

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1answer
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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
37 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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0answers
388 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 ...
2
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0answers
39 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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0answers
134 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, ...
4
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0answers
56 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 ...
3
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1answer
243 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
900 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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0answers
837 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 ...
2
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1answer
2k 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 ...
9
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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
302 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 ...
2
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1answer
228 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 ...
5
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1answer
165 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 ...
2
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0answers
114 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
490 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
45 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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0answers
163 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
696 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?
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 ...
3
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1answer
124 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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1answer
708 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 ...
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2answers
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.
4
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1answer
106 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
391 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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