69

Crystallin proteins are found in the eye lens (where their main job is probably to define the refractive index of the medium); they are commonly considered to be non-regenerated. So, your crystallins are as old as you are! Because of this absence of regeneration, the accumulate damage over time, including proteolysis, cross-linkings etc., which is one of ...


49

Proteases are enzymes in your digestive system that help break down food, acting like molecular-sized scissors that cut up proteins. Proteases have clefts, or subpockets, into which proteins fit, where the substrate (protein) gets cut. Infectious or pathogenic prions are resistant to proteases, because of their three-dimensional conformation, or shape, ...


32

You are correct in thinking that since the translation of mRNA begins with AUG, which codes for methionine, then all proteins should contain a methionine at their N-terminus (aka start site). But, it is indeed not so. First of all, I want to mention about variations in start codon. As you say, AUG is not the only, but actually the most common, start codon, ...


32

It is highly unlikely that there exist any protein that is made from completely identical nucleotide sequences across the entire human population. There will certainly be regions within a gene that are highly conserved, but there is little evolutionary pressure to conserve an entire gene's nucleotide sequence across the population. This is in part due to ...


31

Proteins can move around the membrane. Most proteins do move within the membrane. The membrane is a liquid crystal and has fluid behaviour. Specifically, this is due to the membrane being in a gel-state. This gel state allows phase behaviour which means that the protein is able to move around on the surface. This results in an effect that is often referred ...


28

Because their shape reminded researchers of rolls of Sushi (Ichinose et al, 1990): These repeats were initially called GP-I structures because they were first identified in $\beta_2$-glycoprotein I. More recently, they have been called short consensus repeats or sushi structures because of their shape.


22

I like Mowgli's answer, because it is a non-obvious example. However I would also point out that there are many, many protein-based structural components in the body that we know do not regenerate due to associated pathologies; so presumably these structural proteins are as old as from when they first arose in developemnt. Take the stereocilia on hair cells ...


20

Well you are assuming one sequenced genome/proteome per NCBI tax id. That is no longer true. So if you click on the proteome filter it decreases by half. Which gets you into the 60,000 range. Now not all of these are "different" conceptual proteins, many are artifacts from the way GenBank/EMBL/DDBJ interact with the TrEMBL section of UniProtKB i.e. they are ...


20

Humans have many variants There is variation. The project I use to help understand this natural variation is gnomAD. Using VarMap and a slightly out of date gnomAD file, I counted 16007805 protein-coding variants across the human genome. This number will only go up over time. Indeed, the 1000 Genome project found that on average each person has between ...


19

6405 proteins mapping to 5220 genes, according to Ensembl. In Ensembl's BioMart, you can select the PDB ID as external reference. Export the results and count the unique proteins/genes that have a PDB ID.


18

The only difference between FPLC and HPLC is the amount of pressure the pumps apply to the column. FPLC columns have a maximum pressure of about of 3-4 MPa, whereas HPLC columns can withstand or require much higher pressures. As a general rule, HPLC columns won't work with old FPLC equipment; FPLC columns can go on HPLCs as long as the pressure can be ...


17

It has been well established that mRNA abundance serves as a poor proxy for protein abundance in most cases. This paper on yeast and this paper on cancer both establish this, although using older techniques (SAGE and microarrays, respectively), while this more recent review discusses the topic in light of more recent technologies (e.g. RNA-seq). Perhaps the ...


17

EDIT: Thanks a lot to @abukaj for pointing out the mistake in my answer (and to @paracetamol for asking such a beautiful question). I am rewriting my answer to incorporate the (hopefully) correct background knowledge this time. NEW ANSWER: As @paracetamol and @AlanBoyd (in their answer) pointed out the lack of credible support for the claim that infants ...


15

Since you chose kinesins as an example class of motor proteins, I will also stick to them. In general, the movement mechanisms of kinesins are well studied and the general structure of kinesin proteins, that is a dimer, is known by crystallography (see Kull et al. (1996) for the structure publication). Even before that, the movement of single kinesin ...


14

IDPs are indeed attractive drug targets and there are ongoing efforts to develop drug molecules that block interactions between a disordered and a structured protein. According to this relatively recent paper, however, these efforts have not brought a drug on the market, yet. A few promising studies have shown drug-like molecules that inhibit protein-...


14

The formation of protein complexes or aggregates in aqueous buffers is determined by a number of factors: physical properties of the protein itself, pH, temperature, type and concentration of the used cosolvent (salt). Solutes are often roughly divided by type into chaotropes ('disorder-making'), which destabilise protein structures and kosmotropes ('order-...


14

Ramachandran plots show the relationship between the phi and psi angles of a protein referring to dihedral angles between the N and the C-alpha and the C-alpha and the C-beta. As an aside, the omega angle between the C-beta and the N tends to be fixed due to pi-pi interactions. Dihedral Angles There are limits to possible distributions of phi and psi ...


14

The answer is chance or, even better, contingency. About your calculations, it is true that the theoretical sequences are almost unlimited, but the basic scaffolds are not. Very different sequences can fold into the same basic scaffold and have a similar reactivity/function. So, even if not all the sequences have been explored on this planet, most of the ...


13

It's just so much more convenient to have the enzymes ready without having to thaw them. The main reason you freeze enzymes is to keep them active, if you figure out a buffer that keeps them unfrozen without compromising activity, that is a huge increase in convenience. Not having to thaw the enzymes before use saves a lot of time, if you can manage to keep ...


13

The protein is called rhodopsin and the bit that gets kinked up is called retinol. Normally when light hits it, it does trans to cis isomerization at the 11th carbon. 'kinks up' is a pretty apt way of describing it. I'm not familiar with the shipped down to the liver part, but I'm guessing that the photo reaction of the retinol with itself or the ...


13

Overview Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures. How do you know when you get it right? Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring a ...


12

PDB is a good resource for answering such questions, since it will let you filter results by many additional parameters. To count and extract 3D structures of human proteins: Open Advanced search tab of the PDB website. Select Biology -> Source organism from the menu. Type Homo sapiens (human). You can reduce redundancy by checking Remove Similar Sequences ...


12

As nobody has answered this good question, I'll have a go. Firstly, let me state that I have little-or-no knowledge of heat-shock proteins. What follows are some general observations and thoughts. It would not be unusual for the same enzyme from different species to have different kinetic properties. For example, yeast and horse liver alcohol ...


12

These are completely different concepts, which sometimes may be connected. A motif in biology is a mathematical model, typically of a sequence, that predicts which sequences belong to some defined group. For example, a DNA sequence motif can characterize the binding site of a transcription factor, i.e. which sequences tend to be bound by this factor. For ...


12

Short Answer There is no agreed upon naming convention for proteins - there are some rough standards because in language people usually try to convey their ideas in a way others can understand, but that doesn't necessarily mean fixed rules. Longer Answer I think it's important to recognize the process for understanding what proteins do is not always ...


12

TLDR: As far as I know, there's no specific reason some proteins are called "factors"; it's just a matter of what name was chosen. "Protein" is a specific term meaning a long chain of amino acids. They are typically at least 50 amino acids long. Conversely, the word "factor" is quite a loose term and is as broad as even being "an element of something". So, ...


11

No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are: Genes (eukaryotic genes anyway) are spliced to produce mRNA, a process that removes introns and leaves only the exons. If you just translate the entire chromosome file you will get noise. Splicing also changes ...


11

The paper's description is poor, but they seem to be describing an encoding where each of 20 possible amino acids are associated with a position within a string of 20 bits, e.g. alanine with offset 0, cysteine with offset 1, etc. With that representation, one amino acid residue within a window is encoded by a string of 20 bits, 19 of them being 0 and the ...


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