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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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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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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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