9

There is a clear explanation and figure showing this in the following reference: Anton Gorkovskiy, Kent R. Thurber, Robert Tycko, Reed B. Wickner, PNAS 2014, 111 (43) E4615-E4622. A parallel beta sheet is one where the direction from N- to C-termini on adjacent strands run in a parallel direction (rather than antiparallel). In-register means that each ...


6

Yes, the arginine side chain is an excellent hydrogen bond donor. Charged N-H groups are even better hydrogen bond donors than the corresponding neutral N-H groups. Here is an article that gives examples of arginine side chains in hydrogen bonds. It showcases bidendate hydrogen bonds (i.e. two hydrogen bonds from the arginine side chain) with carboxylates ...


5

According to the Oxford dictionary, a machine is: An apparatus using mechanical power and having several parts, each with a definite function and together performing a particular task. Based on that definition, I think some proteins and enzymes could definitely be considered machines. A good example for that, in my opinion, would be ATP Synthase and all ...


5

Who was responsible for this naming system and how can we change it? Michael Faraday was responsible for the terms anode and cathode more than hundred years ago. All the confusion regarding the nomenclature will vanish if you do not associate electrostatic signs with these two terms. One should identify the electrode labels with the redox processes rather ...


4

Glycoproteins come in O-linked and N-linked forms. For O-linked sugars, a glycosidic bond forms between the sugar and the hydroxyl of a serine or threonine side chain. For N-linked sugars, a glycosidic bond forms between the sugar and the amide of asparagine. The equilibrium for all these reactions lies on the side of hydrolysis in aqueous solution. Is it ...


3

In milk, casein exists as a colloidal aggregate (casein micelle) with the properties you state, but purified casein is different. It is rich in proline (shown below), has no disulfide bridges, and hence little tertiary structure to hide the hydrophobic residues in the core of the protein with the hydrophilic residues on the surface to bind to water. In ...


2

You can conveniently normalize the peak height to unity, if your sole purpose is to compare the peak shapes. It is not forbidden at all. However you should not attempt any quantitation. You can read the paper here Total peak shape analysis: detection and quantitation of concurrent fronting, tailing, and their effect on asymmetry measurements


2

I assume you have a UV/Vis absorbance based measurement. Then the absorbance should follow Beer´s Law which states that absorbance is proportional to concentration. Therefore you should be fine with your normalization approach. You could check if you are in the linear range by performing a calibration.


2

This is a great introduction to the concept of lack of precision (ie error) in measurements. It is unlikely that your volumes are exactly 5 mL and 6 mL or that your protein concentrations are exactly 20 mg/mL and 18 mg/mL. The errors in these measurements combine to give different calculated protein amounts even though the protein amounts are presumably the ...


2

The good mnemonic tool to remember is : Anode = anabasis, electrons would be going upwards from the electrode to the wire = oxidation, ( Xenophon, Anabasis, 404BC, "The journey upwards(to north)) Cathode = cathabasis(the journey downwards), electrons would be going downwards from the wire to the electrode = reduction That means a cathode/anode is the ...


2

When a reaction is at equilibrium, there will be stochastic fluctuations. These are usually not measurable (for example, if we have more than a mole of products and reactants in our reaction mixtures). In this specific case, the fluctuations are easy to measure because the total number of antigen molecules per cell is countable, and you are separating cells ...


1

Dynamics can mean many things, and not all proteins undergo extensive conformational changes during their lifetime. Some are fairly rigid in solution. XRD or NMR data represents an average over the conformations of a protein construct sampled under experimental conditions. A protein construct is a variant of the protein, selected to allow expression and ...


1

Definition Protein backbone dihedral angles are called φ (phi), involving the backbone atoms COn-1 - Nn - Cαn - COn , ψ (psi) involving the backbone atoms Nn - Cαn - COn - Nn+1) and ω (omega) involving the backbone atoms Cαn - COn - Nn+1 - Cαn+1). Thus, φ controls the COn-1 - COn distance, ψ controls the Nn - Nn+1 distance and ω controls the Cαn - Cαn+1 ...


1

should I recalculate the dilutions to get the concentration 2 mg/mL in total with the reagent added? Either way works as long as you are consistent. Plot dilute concentration You can use the final concentration in the cuvette and plot this against the measured absorbance. When you use this standard curve, it will also give you concentration of your ...


1

Your question is about immobilized metal affinity chromatography (IMAC), often used to separate a protein expressed in the E. coli bacterium from other proteins made by it. The protein of interest is expressed with a histidine-containing affinity tag which binds to immobilized nickel or cobalt at neutral or basic pH. Immobilization is achieved by complexing ...


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