1430: Proteins - Revision history

172.68.126.139: Noted real-life relevance of title text

2024-08-22T05:09:10Z

Noted real-life relevance of title text

172.69.6.129: /* Explanation */

2024-01-20T22:49:47Z

‎Explanation

Kynde: /* Explanation */

2024-01-15T07:56:27Z

‎Explanation

Kynde: /* Explanation */ Mentoning the conversation in panel 2 which was not in the explanation

2024-01-15T07:56:16Z

‎Explanation: Mentoning the conversation in panel 2 which was not in the explanation

LostXOR: Pointed broken link to Wayback Machine

2023-04-06T19:43:06Z

Pointed broken link to Wayback Machine

Theusaf: Reverted edits by Donald Trump (talk) to last revision by CRLF

2022-05-26T20:00:22Z

Reverted edits by Donald Trump (talk) to last revision by CRLF

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Donald Trump: Reverted edit by anti-crap user

2022-05-26T19:02:53Z

Reverted edit by anti-crap user

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2022-05-26T18:03:21Z

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Donald Trump: Reverted edit by anti-crap user

2022-05-26T17:04:57Z

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2022-05-23T18:42:30Z

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@@ Line 22: / Line 22: @@
 Megan replies "if you can fold a Protease enzyme;" these are proteins whose job it is to break down (i.e. "cut") other proteins, often in very specific ways. In this manner, Protease enzymes are analogous to extremely specialized scissors, so Megan is effectively saying "You can make cuts if you can fold yourself a pair of scissors." Of course, when trying to predict the folding trajectory in nature of a protein A, and one is allowed to make cuts during the process, one is making the assumption that the Protease that cut protein A is already folded and functional. In other words, making cuts while folding might actually make the process ''more'' complicated, not less, as now you have to consider how the cutting enzyme is folded, too.
-The title text refers to the result of folding a flapping bird in origami. By pulling the tail, the head will move forward and down. However, since the joke is about folding proteins, this idea is extrapolated to include the folded proteins. The C-terminus (end of the protein chain), in this case analogous of the tail, if "pulled" would cause a created cavity or tunnel to squeeze, much like pulling a knot would do the same.
+The title text refers to the result of folding a flapping bird in origami. By pulling the tail, the head will move forward and down. However, since the joke is about folding proteins, this idea is extrapolated to include the folded proteins. The C-terminus (end of the protein chain), in this case analogous of the tail, if "pulled" would cause a created cavity or tunnel to squeeze, much like pulling a knot would do the same. In general, protein conformational changes where parts of a protein change shape as a result of pushing or pulling on another part of the protein are common in biological systems (eg, {{w|Allosteric regulation|allosteric regulation}}, {{w|Cooperative binding|cooperative binding}}).
 {{w|Folding@Home}} (F@H) is a distributed computing project which aims to simulate protein folding for research purposes. Rather than the traditional model of using a supercomputer for computation, the project uses idle processing power of a network of personal computers in order to achieve massive computing power. Individuals can join the project by installing the F@H software (there is also a web version that can be run using Google Chrome) and are then able to track their contribution to the project. Individual members may join together as a team, with leaderboards measuring team and individual contributions.

@@ Line 16: / Line 16: @@
 Cueball then asks Megan why it is such a hard computational problem; Megan's response is to ask Cueball if he's ever {{w|Origami|folded paper}} to make a {{w|Crane (bird)|crane}}. When he responds in the affirmative, she then compares the problem of predicting protein folding to creating a ''living'' crane by the paper-folding process. The analogy is that a protein cannot just fold to a figurative representation of a bio-molecule, the way a paper crane superficially resembles a live crane; the protein must assume an exact, perfect fold in order to be functional.
-{{w|Levinthal's paradox}} is a thought experiment, also constituting a self-reference in the theory of protein folding. In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. For example, a polypeptide of 100 {{w|Residue (chemistry)|residue}}s will have 99 peptide bonds, and therefore 198 different {{w|Dihedral angle|phi and psi bond angles}}. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3<sup>198</sup> different conformations (including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation. This is true even if conformations are sampled at rapid (nanosecond or picosecond) rates. The "paradox" is that most small proteins fold spontaneously on a millisecond or even microsecond time scale. This paradox is central to computational approaches to protein structure prediction.
+{{w|Levinthal's paradox}} is a thought experiment, also constituting a self-reference in the theory of protein folding. In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. For example, a polypeptide of 100 {{w|Residue (chemistry)|residue}}s will have 99 peptide bonds, and therefore 198 different {{w|Dihedral angle|phi and psi bond angles}}. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3<sup>198</sup> different conformations (including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation. This is true even if conformations are sampled at rapid (nanosecond or picosecond) rates. The "paradox" is that most small proteins fold to their proper conformation spontaneously, on a millisecond or even microsecond time scale. This paradox is central to computational approaches to protein structure prediction.
 As Cueball mentally turns over the hypothetical process of folding paper to make a living crane, he wonders if he is allowed to perhaps "cut" the paper to make more complicated folds available. In origami, purists [https://web.archive.org/web/20200207151442/http://www.barf.cc/jeremy/origami/BOOK/essays/origami_purism/origami_purism.htm] considered it as cheating if you cut the paper or use more than one sheet of paper, which is why Cueball asked if he was 'allowed' to do such in the hypothetical exercise they are discussing.

@@ Line 12: / Line 12: @@
 {{w|Protein folding}} is the process by which proteins, which are floppy, unstructured chains of {{w|amino acids}} when initially synthesized in a cell, assume a stable, functional shape. If the folding process does not complete, or completes incorrectly, the resulting protein can be inactive or even toxic to the body. Misfolded proteins are responsible for several {{w|neurodegenerative}} diseases, including {{w|Alzheimer's disease}}, {{w|amyotrophic lateral sclerosis}} (ALS), and {{w|Parkinson's disease}}, as well as some non-neurodegenerative diseases such as cardiac amyloidosis.
-Cueball asks Megan is that is a hard problem, to which she replies, that someday someone may find a harder problem. Thus she indicates that at present time, this is the hardest problem in the world! That is saying a lot.
+Cueball asks Megan if that is a hard problem, to which she replies, that someday someone may find a harder problem. Thus she indicates that at present time, this is the hardest problem in the world! That is saying a lot.
 Cueball then asks Megan why it is such a hard computational problem; Megan's response is to ask Cueball if he's ever {{w|Origami|folded paper}} to make a {{w|Crane (bird)|crane}}. When he responds in the affirmative, she then compares the problem of predicting protein folding to creating a ''living'' crane by the paper-folding process. The analogy is that a protein cannot just fold to a figurative representation of a bio-molecule, the way a paper crane superficially resembles a live crane; the protein must assume an exact, perfect fold in order to be functional.

@@ Line 12: / Line 12: @@
 {{w|Protein folding}} is the process by which proteins, which are floppy, unstructured chains of {{w|amino acids}} when initially synthesized in a cell, assume a stable, functional shape. If the folding process does not complete, or completes incorrectly, the resulting protein can be inactive or even toxic to the body. Misfolded proteins are responsible for several {{w|neurodegenerative}} diseases, including {{w|Alzheimer's disease}}, {{w|amyotrophic lateral sclerosis}} (ALS), and {{w|Parkinson's disease}}, as well as some non-neurodegenerative diseases such as cardiac amyloidosis.
-Cueball asks Megan why it is such a hard computational problem; Megan's response is to ask Cueball if he's ever {{w|Origami|folded paper}} to make a {{w|Crane (bird)|crane}}. When he responds in the affirmative, she then compares the problem of predicting protein folding to creating a ''living'' crane by the paper-folding process. The analogy is that a protein cannot just fold to a figurative representation of a bio-molecule, the way a paper crane superficially resembles a live crane; the protein must assume an exact, perfect fold in order to be functional.
+Cueball asks Megan is that is a hard problem, to which she replies, that someday someone may find a harder problem. Thus she indicates that at present time, this is the hardest problem in the world! That is saying a lot.
 {{w|Levinthal's paradox}} is a thought experiment, also constituting a self-reference in the theory of protein folding. In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. For example, a polypeptide of 100 {{w|Residue (chemistry)|residue}}s will have 99 peptide bonds, and therefore 198 different {{w|Dihedral angle|phi and psi bond angles}}. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3<sup>198</sup> different conformations (including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation. This is true even if conformations are sampled at rapid (nanosecond or picosecond) rates. The "paradox" is that most small proteins fold spontaneously on a millisecond or even microsecond time scale. This paradox is central to computational approaches to protein structure prediction.

@@ Line 16: / Line 16: @@
 {{w|Levinthal's paradox}} is a thought experiment, also constituting a self-reference in the theory of protein folding. In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. For example, a polypeptide of 100 {{w|Residue (chemistry)|residue}}s will have 99 peptide bonds, and therefore 198 different {{w|Dihedral angle|phi and psi bond angles}}. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3<sup>198</sup> different conformations (including any possible folding redundancy). Therefore, if a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to arrive at its correct native conformation. This is true even if conformations are sampled at rapid (nanosecond or picosecond) rates. The "paradox" is that most small proteins fold spontaneously on a millisecond or even microsecond time scale. This paradox is central to computational approaches to protein structure prediction.
-As Cueball mentally turns over the hypothetical process of folding paper to make a living crane, he wonders if he is allowed to perhaps "cut" the paper to make more complicated folds available. In origami, purists [http://www.barf.cc/jeremy/origami/BOOK/essays/origami_purism/origami_purism.htm] considered it as cheating if you cut the paper or use more than one sheet of paper, which is why Cueball asked if he was 'allowed' to do such in the hypothetical exercise they are discussing.
+As Cueball mentally turns over the hypothetical process of folding paper to make a living crane, he wonders if he is allowed to perhaps "cut" the paper to make more complicated folds available. In origami, purists [https://web.archive.org/web/20200207151442/http://www.barf.cc/jeremy/origami/BOOK/essays/origami_purism/origami_purism.htm] considered it as cheating if you cut the paper or use more than one sheet of paper, which is why Cueball asked if he was 'allowed' to do such in the hypothetical exercise they are discussing.
 Megan replies "if you can fold a Protease enzyme;" these are proteins whose job it is to break down (i.e. "cut") other proteins, often in very specific ways. In this manner, Protease enzymes are analogous to extremely specialized scissors, so Megan is effectively saying "You can make cuts if you can fold yourself a pair of scissors." Of course, when trying to predict the folding trajectory in nature of a protein A, and one is allowed to make cuts during the process, one is making the assumption that the Protease that cut protein A is already folded and functional. In other words, making cuts while folding might actually make the process ''more'' complicated, not less, as now you have to consider how the cutting enzyme is folded, too.