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The LOV protein structure contains a Jα- and an Aʹα-helix. Would “A prime alpha helix” be the correct pronunciation for Aʹα-helix?

I'm speaking soon in front of the scientists in the field that I really admire and English isn’t my first language. I don’t want to embarrass myself.

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    $\begingroup$ Andrea this is not really a chemistry question... Do not worry to much about the pronunciation, if they are as good scientist as you suggest, they will know English is not your mother tongue and would understand you presentation if it is properly prepared. $\endgroup$
    – PAEP
    Commented Jul 3, 2023 at 15:34
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    $\begingroup$ @PAEP I'm sorry to decline your edit, but there is virtually no reason to use MathJax for the letter α, especially in title. Unicode would do better since alpha should be upright, not slanted (there is no upgreek alternative for MathJax). $\endgroup$
    – andselisk ♦
    Commented Jul 3, 2023 at 16:23
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    $\begingroup$ I would think the question is pretty much OK for Chemistry.SE, specifically having How to pronounce "potassium manganate(VII)"?, How do you pronounce GAMESS or How to pronounce G°? Personally, having very limited biochem background, I find OP's pronunciation perfectly fine. $\endgroup$
    – andselisk ♦
    Commented Jul 3, 2023 at 16:23
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    $\begingroup$ Given short videos like Exploring different optogenetic systems: Photocaging authored by EMBL, are there colleagues of yours already in the field presenting results similar enough, perhaps in seminars / remote webinars (for the later I infer from small molecule chemistry and what the e.g. the American Chemical Society offers to its members)? $\endgroup$
    – Buttonwood
    Commented Jul 3, 2023 at 17:10

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As andselisk declared in his comment, OP's pronunciation of "A-prime alpha helix" is perfectly fine. I just wanted make a few points here, which would help OP's speech if he/she choose to use my reference here. According to following reference (Ref.1):

  1. N-terminal helix is A'$\alpha$ (pronounce as N-terminal A-prime alpha helix).
  2. Further, C-terminal helix is J$\alpha$ (pronounce as C-terminal J alpha helix).

In between there are 4 more helices (C$\alpha$, D$\alpha$, E$\alpha$, and F$\alpha$).

References:

  1. Vladimir Arinkin, Joachim Granzin, Katrin Röllen, Ulrich Krauss, Karl-Erich Jaeger, Dieter Willbold, and Renu Batra-Safferling, "Structure of a LOV protein in apo-state and implications for construction of LOV-based optical tools," Scientific Reports 2017, 7, Article number: 42971 (10 pages) (DOI: https://doi.org/10.1038/srep42971).
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    $\begingroup$ Please don't use long obsolete even by the LaTeX standards two-letter macros such as \bf. I'm not sure MathJax is appropriate here at all. The letter alpha should be upright, not italicized, and it's something you cannot do without hackery in MathJax. Bold text in CM font normally implies a vector, and if you want to emphasize the letter, I'd do it via secondary means such as phonetic transcription in the spelled-out part. Finally, "Hope this'd help." is just noise. $\endgroup$
    – andselisk ♦
    Commented Jul 3, 2023 at 22:49
  • $\begingroup$ @andselisk Hello andselisk. Should quantities that have subscript/superscript belonging to sum indexes be upright? For example, for the Christoffel's symbol of the 2nd kind, it is $\Gamma_{\mathrm{ij}}^\mathrm{k}$ or $\Gamma_{ij}^k$? For a sum, should we write $\sum_i a_i$ or $\sum_\mathrm{i} a_\mathrm{i}$? $\endgroup$
    – Metal Storm
    Commented Jul 3, 2023 at 23:42
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    $\begingroup$ @MetalStorm In both these cases the indices are italicized. However, for example in the symbol for ionic radius $R_\mathrm{i}$ the index is upright because it's a descriptive one. See Which symbols are written in roman (upright) font and which are italicized? and references therein. $\endgroup$
    – andselisk ♦
    Commented Jul 4, 2023 at 6:40
  • $\begingroup$ @andseliks Hello andselisk, sorry to interrupt you with nothing that has to do with the question. Do you know how to use a package like \pu{} in LaTeX? I use the TexStudio editor. I do chemical engineering, so we write much more numbers than chemistry, and now that I know the \pu{} package it would be nice to have something similar. This page unfortunately shows a package too old that won't be compiled. Thank you very much in advance. $\endgroup$
    – Metal Storm
    Commented Jul 6, 2023 at 12:22
  • $\begingroup$ @MetalStorm \pu is the macro for physical units bundled with mhchem for MathJax and is not available in original mhchem, the LaTeX package. If you are compiling a LaTeX document, consider loading siunitx package to help with typesetting quantities correctly. $\endgroup$
    – andselisk ♦
    Commented Jul 8, 2023 at 11:33

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