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Ar means aromatic and + means positively charged residues. However, this is not a standard code (as of now). From the same paper: Sequences closely matching these optimal binding motifs, R-X-[Ar/S]-[+]-pS-[LEAM]-P and R-[S/Ar]-[+]-pS-[LEAM]-P, denoted as mode 1 and mode 2 consensus sequences, were found to be present in many known 14-3-3 ligands ( Yaffe ...


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I used to work for a company well-known for its modification state-specific antibodies, including phospho-specific ones, and they actually performed extensive in-house testing of PBST vs. TBST in Western blotting. Part of the reason the company chose to recommend the use of Tris-buffered saline over phosphate-buffered saline based buffers was the clearly-...


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Yep, that is correct in general. However, sometimes proteins indirectly determine phenotype. For example, the skin colour is dependent on melanin (not a protein) but the melanin producing cells work because of proteins. Further, melanin production is also controlled by proteins. Thus, skin colour is not DIRECTLY determined by proteins but because proteins ...


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Generally speaking, structure prediction programs look only at the thermodynamic minimum, without consideration of the kinetic trajectory of folding. The main reason for this is mostly time considerations. It's very difficult to accurately model the true folding pathway of even a moderately sized protein. With special tricks and a bunch of computing power, ...


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Beta sheets and alpha helix are secondary structures that are simply very common to proteins. Their formation depends on the Amino acids that make up particular stretch in the primary sequence. For example alanines in a row will naturally tend to twist up into a alpha helix in water (medium matters). There are no hard and set rules to determine Tert. ...


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Bacteria and plants are able to synthesize all amino acids, as they are capable of nitrogen fixation. If animals eat plants, they get the essential amino acids needed for their proteins. Humans get the essential amino acids by eating these animals or directly by consuming plants. So yes, it is a never-ending cycle of passing.


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From the mention of “aromatic residues” in the figure legend (in a different context) I assume Ar stands for aromatic residues. Ar is certainly not an abbreviation for arginine. I would guess that [H/+] means either histidine or any positively-charged residue. I think that the authors of the paper should have pointed this out in the figure legend, and that ...


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A motif is a pattern that you discover in a structure by analysis. For example, common sequence motifs are short sequence fragments with parts similar to a regular expression. So, if you have a motif like "A*C" this matches to the sequences "AAC" and "ACC" but not to "ACA". You can reverse the process to discover the motif from the sequences. Similarly with ...


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The optimum pH for catalase can be found be a simple search. According to the Wikipedia entry for catalase it is approximately 7. With the exception of extreme pHs, which can cause denaturation, the pH optimum of enzymes is often related to the ionization of the amino acid residues that participate in the reaction (and hence their pKa). Often what happens ...


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A general note on phenotype I think that the meaning of phenotype has become more complicated over time compared to what it was when it was first coined. As you said, in simple words, a phenotype is an observable characteristic of an organism. However, for Mendel, an observable characteristic would have been only an obviously gross change in the morphology ...



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