Questions tagged [proteins]

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

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3
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74 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
472 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 ...
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2answers
656 views

Why aren't chaperones considered 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 ...
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1answer
4k 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 $\mathrm{d^6}$...
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1answer
2k 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
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1answer
355 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
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1answer
1k 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
201 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
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1answer
229 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 ...
5
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1answer
279 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 a lot of ...
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1answer
94 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
474 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 ...
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0answers
85 views

Do proteins have a smell?

Proteins are heavy and not so volatile. Does it mean that pure proteins do not have a smell?
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3answers
2k 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: ...
2
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0answers
39 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 ...
2
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2answers
4k 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
1k 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 ...
2
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1answer
9k 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
84 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 ...
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1answer
282 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
461 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 ...
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1answer
674 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
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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386 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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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 ...
4
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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 ...
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133 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, ...
3
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1answer
238 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 ...
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3answers
872 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
819 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
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 ...
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4answers
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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 ...
5
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1answer
301 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
226 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
127 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 (...
5
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1answer
161 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 ...
4
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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
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
482 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 ...
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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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162 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
692 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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852 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 ...