Talk:Protein folding

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This article was the subject of a Wiki Education Foundation-supported course assignment, between 1 September 2020 and 17 December 2020. Further details are available on the course page. Student editor(s): Calhobbs11. Peer reviewers: Vazi97, Jimmyjohnslaser.

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Wiki Education Foundation-supported course assignment

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"misfolded (incorrectly folded)"

Is this really necessary? Most people know what the prefix "mis" means. —Preceding unsigned comment added by 81.102.52.2 (talk) 17:03, 23 November 2010 (UTC)

Remove Dual Polarization Interferometry?

This is a relatively obscure technique with little to do with protein folding. Only 39 articles on Pubmed deal with DPI and only 2 of these deal loosely with protein folding. By comparison, there are 3138 using NMR which is not discussed in the article. Also, the text seems to be taken verbatim from the DPI article --Biophysik (talk) 04:51, 4 May 2009 (UTC)

Most protein folding occurs in the ER lumen, and I think this article implies it happens in the cytosol, which is a very different environment. Can someone back me up here? I think it should be changed. —Preceding unsigned comment added by 24.13.229.19 (talk) 15:45, 29 September 2008 (UTC)

This is just a feedback: the link for the third reference,

Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; Web content by Neil D. Clarke (2002). "3. Protein Structure and Function", Biochemistry. San Francisco: W.H. Freeman. ISBN 0-7167-4684-0.

does not work. Delete this comment when solved. —Preceding unsigned comment added by 217.126.167.93 (talk) 09:43, 13 August 2008 (UTC)

Is there a way to simplify the explanation of the process? The 'middle-school English' explanation (which of course, has since been deleted)was actually a good summary without having to go deep into the complexity.

I'm not sure my biochemistry is up to it, but should something about the different levels of protein structure be added here, (primary, secondary, tertitary etc.)?

The main protein article has that - I suppose you could refer to that article. -- Marj 05:44, 26 Oct 2003 (UTC) ok

I've tried to make the initial section a bit clearer but it's a difficult thing to provide a non-technical summary of. I've also put in some references to (mostly) free articles & books. Hopefully it doesn't jump in quite so quickly now. See what you think. MockAE 12:34, 14 April 2007 (UTC)

Folding temperature

I have read that the folding temperature of a protein is defined as the temperature at which there is a peak in the heat capacity of the protein. I am not sure what this means physically about what is different in the protein at the folding temperature versus below the folding temperature. However, I would like very much to know. Thank you. —Preceding unsigned comment added by Shindizzle (talk • contribs)

This page is useless. If anyone could understand this page, they wouldn't need Wikipedia to explain it to them. —Preceding unsigned comment added by 76.215.213.229 (talk)

The folding temperature is a minor point in the grand scheme of protein folding. FYI, it is a characteristic temperature at which the protein spends half the time in the folded state and half the time in the unfolded state. The peak of the heat capacity for any substance (protein or otherwise) is the temperature at which the transition from one state to another occurs (e.g. phase transition). So, for proteins, the peak is the temperature at which the protein goes from the unfolded state to the folded state. —Preceding unsigned comment added by 66.122.236.163 (talk)

That's not entirely correct. The temperature at which the protein spends half the time in the folded state and half the time in the unfolded state is the ' folding transition temperature for a two state folding protein '. The term 'folding temperature' is an imprecise term. --159.178.50.165 (talk) 15:41, 10 March 2008 (UTC)

external link to rosetta is needless- they do not study the protein folding. they predict final structure, ant this should be addressed to "protein structure prediction" . this also refers to human proteom folding project, predictor at home, fight aids at home and all others. only Stanford is studying the protein folding. 84.15.64.164 12:30, 8 May 2006 (UTC)Samurajus712

H-bonds, entropy, etc.

This is a nice article, although it could be done more "in depth". H-bonds do stabilize protein structure. The catch: water is liquid. When water freezes itself, there is a certain energy gain called enthalpy of fusion. This enthalpy of fusion originates mostly from formation of H-bonds between molecules of water: these H-bonds are strong in the solid state, but "transient" in the liquid mobile water. Same thing with protein folding, helix-coil transitions, crystallization, etc. The energy of H-bond in protein folding is ~-1.5 kcal/mol (mutagenesis and other data). Main force that opposes protein folding is conformational entropy (like in any other liquid to solid state type transition). This is easy to fix. I can do this later. Biophys 17:26, 28 October 2006 (UTC)

Techniques for studying protein folding

It would be good to separate experimental and computational techniques. There are many more experimental methods that should be mentioned here. Biophys 18:03, 29 October 2006 (UTC)

I noticed this also. It seems that there is a lack of flow and continuity in this section. The first three methods mentioned are experimental, then the article talks about computational methods, and finally switches back to experimental methods. If it's alright I'm going to clean this up.Dopeytaylor (talk) 18:03, 14 March 2011 (UTC)

I have reorganized this section, splitting it into two, and reordering a few things. I'm still not satisfied with it. (Dopeytaylor (talk) 18:09, 14 March 2011 (UTC)

It is important to tell something about protein folding pathways based on experimental data (intermediates, transition states, etc.), about thermodynamic stability of proteins, and differences between water-soluble and transmembrane proteins. Beta-sheet is not a secondary structure! The beta-strand is. Biophys 04:08, 2 November 2006 (UTC)

Disulfide bonds often exist within beta sheets, and sometimes even within alpha helices. This is corrected. Biophys 02:07, 4 November 2006 (UTC)

Random coil --> Random coil (protein folding)

Does anyone else think it might be useful to split the random coil article into 2 separate articles? With the first being used to describe the mathematical theory, and the second to describe the protein related aspects of the model?--69.118.143.107 (talk) 18:32, 30 December 2007 (UTC)

Another useful study

The following paper may contain useful material for this article:

Igor V. Grigoriev; Sung-Hou Kim. Detection of Protein Fold Similarity Based on Correlation of Amino Acid Properties. Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 25. (Dec. 7, 1999), pp. 14318-14323. Stable URL: http://links.jstor.org/sici?sici=0027-8424%2819991207%2996%3A25%3C14318%3ADOPFSB%3E2.0.CO%3B2-B

128.197.150.162 (talk) 19:08, 27 October 2008 (UTC) "Iceberg" protein refolder: In the physical point of view, "ice" is a kind of "pure mineral rock", and it can not growing up at the coexistence of other materials. In the process of freezing, salt is drived out and departs from water. In the refolding process，the Solute, that is denaturant such as urea(density is 1.33) and Guanidine(density is 1.34), is also affected by temperature. And the density of active protein is around 1, so the protein stay near the solution uper layer. This directly leads to a decline of the denaturant concentration in the solution. Thus, we obtain two “reductions”- the reduction of thermal movement (this can greatly reduce the probability of peptides entanglement) and the reduction of denaturant concentration at the same time—the two most essential conditions in protein refolding. This creates an excellent condition for protein refolding, that is, low-temperature and a smooth decline in denaturant gradient. Taking the physical and chemical properties of peptide into consideration, the two terminals of the chain are carrying different charges ( N-terminal charge is positive， while C-terminal charge is negative). This enables us to use a program-controlled high voltage electric field to adjust peptides’ state in the solution, to restrict their movement, to pull peptide into a "orderly queue" and to prevent peptides from mutual entangling. At the same time this instrment does not exclude any other existing method of protein folding, and can be merged with the existing ways of folding easily, improve the efficiency and reduce the cost of refolding.

2. Freeze-dry protein folding method: this protocol is only suit for those kind of proteins which can be made in frozen powder or cold resistable proteins(such as EGF, IGF).

 1. freeze-dry machine 
 2. 8M urea, 10mM pH8 phosphate buffer, 5mM BME, inclusion body solution, 25 centigrade overnight
 3. Add sucrose 6% weight or other addictives as freezing protection
 4. Standard process freeze-dry the solution
 5. Use wind, high voltage electrostatic way, or little brush to separate the protein powder and the crystal(keep the room humidity low)  
 6. Test the activity  —Preceding unsigned comment added by Hawk 0917 (talk • contribs) 13:00, 2 July 2009 (UTC) 

Evolutionary Aspects of Protein Folding

It would be helpful to discuss the evolutionary aspects of protein folding as well —Preceding unsigned comment added by 216.141.228.112 (talk) 15:45, 1 November 2008 (UTC)

Someone care to explain 'why' people do protein folding? There seems to be a whole lot of information about 'how' but not 'why. —Preceding unsigned comment added by 220.253.207.129 (talk) 11:59, 14 June 2009 (UTC)

Incorrect protein folding and neurodegenerative disease

Should we realy have at the end of this section a list of all important scientists who are involved in this research!?--Gilisa (talk) 11:20, 5 November 2009 (UTC)

I agree that it doesn't make much sense. The same goes for the section "Modern studies of folding with high time resolution". It would be better to provide one or two review articles referencing the same authors at the respective sections. -- Mittinatten (talk) 13:49, 11 November 2009 (UTC)

I removed the names of scientist and added two review articles that I like, maybe we could add more. -- Mittinatten (talk) 20:27, 17 December 2009 (UTC)

"Proving" and "disproving" Anfinsen hypothesis

The following segment seems to be very problematic:

In the seminal research work published nearly four decades ago, C.B. Anfinsen hypothesized that "information dictating the native fold of protein domains is encoded in their amino acid sequence". However, with the explosive amount of protein sequence, structure, and fold data generated since the time of Anfinsen during the omics era, the emerging picture of the protein universe has challenged Anfinsen's dogma, for it has become evident that numerous protein folds have incredible sequence diversity with no consistent "fold code" . In support of this observation, recent studies have shown that proteins with as low as 1-2% sequence identity may still adopt the same native fold, thus defying any tangible encoding of fold-dictating information into protein sequence. The pursuit of the elusive "fold code" has resulted in little more than patterns of amino acid sequence conservations specific to certain proteins, but no finding has been compelling enough to generalize universally or to utilize for biological applications.

In a recent study, scientists from Harvard-MIT have shown that, despite the enormous diversity within protein folds at the level of 1-dimensional amino acid sequence, nature has encoded fold-conserved information at higher dimensions of protein space such as the 2-D (protein contact maps) or 3-D (structure), that are known to be more intricately related to protein folding phenomena. The study published in PLoS ONE illuminated latent fold-conserved information from higher dimensional protein space using network theory approaches. By examining the entire protein universe on a fold-by-fold basis, the study revealed that atomic interaction networks in the solvent-unexposed core of protein domains are fold-conserved and unique to each protein's native fold, thus appearing to be the encoded "signature" of protein domains. This study hence uncovered that the protein fold code is a "network phenomena" in addition to a sequence and structural phenomena as commonly presumed. The discovery of such a protein folding code also confirms Anfinsens Dogma by proving that a significant portion of the fold-dictating information is encoded by the atomic interaction network in the solvent-unexposed core of protein domains.

• Unfortunately, none of the quoted publications actually proves or disproves Anfinsen hypothesis, but tells about unrelated subjects, such as the same "fold" (do not mix with "folding") being encoded by different amino acid sequences, and so on.Biophys (talk) 22:32, 30 June 2010 (UTC)

References

Disordered Proteins

I take issue with the fact that this article seems to assume that all proteins fold into a well defined 3D shape. There are many instances where it is known that large portions of a protein are disordered, or dynamic in their shape. I believe there either needs to be a segment added on "Disordered Proteins". If need be I can help track down citations. Dopeytaylor (talk) 04:05, 15 February 2011 (UTC)

Sure, please see Intrinsically unstructured proteins. Biophys (talk) 05:54, 15 February 2011 (UTC)

Thanks, I see the link in the opening paragraphs of the article now. I think it is enough to satisfy me.Dopeytaylor (talk) 16:45, 14 March 2011 (UTC)

Actually, I still have a problem with the sentence that mentions disorder proteins. The sentence states “The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded ”. I believe many biologists, including myself might, disagree with the notion that, for a protein, or part of a protein to function, it must always have a distinct static three dimensional structure. Performing a quick search I can find at least two papers where it is stated that a functionally important region of a protein is intrinsically disordered.

A Structurally Disordered Region at the C Terminus of Capsid Plays Essential Roles in Multimerization and Membrane Binding of the Gag Protein of Human Immunodeficiency Virus Type 1

Structure of the Dual Enzyme Ire1 Reveals the Basis for Catalysis and Regulation in Nonconventional RNA Splicing

Dopeytaylor (talk) 18:45, 29 March 2011 (UTC)

Experimental techniques for studying protein folding

I noticed that there are no citations for any of the methods used to study protein folding. It is well known that NMR is used to study structure, but I believe that studying folding using NMR is a special case, and warrants at least a few citations. The same goes for the other methods. Can we find some citations where a paper reports details about the steps a protein goes through when folding that have been discovered using the respective method?

I believe this section is also missing what I've always thought was a very important method for studying folding, and thats point wise mutation studies. I think the most common one cited for this the the Fersht study on Barnase. I will add a section on this method. I think this paper might be the best one to cite. if there is a better one, or more, please let me know. Dopeytaylor (talk) 18:59, 29 March 2011 (UTC)

Sure, this is publication by Fersht about Phi value analysis. Phi value analysis should be described in this article in more detail.Hodja Nasreddin (talk) 02:02, 30 March 2011 (UTC)

Good reference material: "The Protein-Folding Problem, 50 Years On"

Anyone who is interested in improving this article should probably look at the review article The Protein-Folding Problem, 50 Years On. Fairly straightforward read, and it contains a lot of up-to-date and useful information. • Jesse V.^(talk) 05:40, 27 November 2012 (UTC)

And let's not forget chaperones. Macdonald-ross (talk) 05:53, 21 September 2013 (UTC)

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CHEM 342 Critique of an Article

I chose to read this article for my bioinorganic chemistry course because I felt that it unified the biological and chemically related teachings that we are attempting to delve into during our MyMolecule projects. This article was well-supported by sources such as articles and studies from Science magazine and trusted journals such as The Journal of Biochemistry and Molecular Biology," and the links that I clicked on to find the articles led me to the webpage on which I could access them. Based on these facts, I would say that this article is well-updated and preserved with sources that contain purely factual information regarding the process by which proteins are folded and research that has been conducted to prove the nature of protein folding. In addition to reliable sources, the information shared on this page is pertinent to the overall understanding of the nature of protein folding. It combines chemistry-oriented knowledge, such as the importance of H+ bonding, and biologically-inclined information, including the connection between misfolded proteins and degenerative disorders including Alzheimer's.

Makbookpro4 (talk) 00:56, 3 September 2016 (UTC)

Proposed Changes

Hello Wikipedia Community! I am a student editor and I have chosen to improve this article. I want to be talking about my proposed changes here on the talk page to hear some feedback from the Wikipedia Community. Please feel free to mention what changes you would like to see on this page and I will try to accommodate that. Any feedback is welcome to my proposed changes.

Proposed Changes: I would like to add more detailed sections on "Driving Force of Protein Folding" involving the hydrophobic effect and some details about Gibbs free energy, enthalpy, entropy, and water's role in protein folding. I would like to mention information about protein folding in vivo specifically about chaperones. I will be adding some misfolding diseases of proteins and advancing the computational methods of protein folding with X-ray crystallography. I will go into external factors that effect protein folding more in depth along with the protein folding energy landscape. I would like to add some foundational backbone to this article for the readers to have a better understanding of what protein folding is. To accomplish this I would like to add some information about protein structure and interactions that contribute to protein folding. I plan to mention primary, secondary, tertiary, and quaternary structure in minimal detail because I find it important to understand what proteins fold into. I also plan to mention the noncovalent forces involved in protein folding with minimal detail (van der Waals forces). These topics I feel are important toward understanding the article, but I am open to suggestions on which topics to put emphasis on and which to hold back on. Thank you. Andrewovak (talk) 20:53, 28 October 2016 (UTC)

Peer Review # 1 Hello! Overall, the article is awesome! I am actually surprised it is just a C class being that it is very in depth and clear. I like the organization of the sections and the summary was concise and touched on all the points present in the article.

There would be some changes that I would add however. I would actually create a whole new section to talk about the various structure levels of protein folding. I know that the definitions are scattered and brief throughout the article but it might be better if it had its own section where the definition could really be explained and shown alongside pictures. Furthermore, for the x-ray crystallography section, I would add some detail regarding what would be considered a good diffraction pattern (i.e. a higher resolution diffraction = smaller distance). I might also add an image of what a diffraction pattern could look like and maybe add a small fun fact that this is also how the structure of DNA was discovered.
In the circular dichoism section, I would stress that each folded protein has a specific signal that can be detected through this method. This technique is therefore utilized to confirm that the protein has folded correctly whereas other techniques like x-ray diffraction are used to discover the protein structure and not really to check folding.
In the end, I think the article is really good and the added changes help fill in the holes. Good job! Kbelardo (talk) 06:17, 22 November 2016 (UTC)

Thank you for your input I implemented the new sections talking about the protein structural levels and it looks more organized! Andrewovak (talk) 01:23, 26 November 2016 (UTC)

Peer Review #2: Hi! Your article was absolutely fantastic! Everything was written both very clearly and concisely. I think that it was really well done in how you were able to write in a way that there was not much confusion as to how protein folding works and for how scientists typically study the protein folding. A couple notes that I would give are on the arrangement and a few other considerations. First, just make sure that when you use comparative or superlatives to describe things, such as when you discussed how "x-ray crystallography is one of the more efficient", make sure that various sources have definitely deemed that because that could come off as bias so it wouldn't hurt to add one more source citation to help readers know that this claim wasn't written lightly. But that's ultimately up to you as long as the main source you cited contained that. For arrangement, although the first section of the page is labelled as "known facts", I think it might be better to put the "incorrect protein folding" and "Levinthal paradox" sections towards the end of the article since these two topics probably don't need to be as focused on, in comparison to your sections of computational methods and experimental techniques. Also, for your other sections under experimental techniques, you can always try and condense the lesser known techniques into a paragraph and just call them as other secondary methods and the primary methods would be the ones you developed more, like x-ray crystallography and fluorescence spectroscopy. But that's more of a stylist choice as it seems like the other techniques only had a sentence, which is fine as well! Overall, great job and I hope my comments were helpful! Tiffanyhu (talk) 21:44, 22 November 2016 (UTC)

Thank you for the organizational suggestion of moving "incorrect protein folding" and "Levinthal paradox" sections towards the end of the article. I agree with this it is mostly unrelated to the topic it was under so I moved it toward the end. Andrewovak (talk) 01:23, 26 November 2016 (UTC)

suggestion to add few pictures

i would like to suggest to add few pictures that could demonstrate the folding in Beta sheets. there are few pics available on googleing , but iam not sure that they are under creative commons license and so am not uploading. but i would like authenticated authors to check the availability and add to the article. http://www.bio.miami.edu/tom/courses/protected/ECB/CH05/5_10.jpg https://biochem1362blog.files.wordpress.com/2014/02/importance_f3.gif http://2.bp.blogspot.com/-Hh_ypr5lljA/Td6dp7ccb6I/AAAAAAAAAEY/CpXHeX1hgXg/s1600/figure4.jpg

or few pics like this — Preceding unsigned comment added by Raj.palgun13 (talk • contribs) 11:57, 6 December 2016 (UTC)

should RNA folding be mentioned, or perhaps have it's own page?/reference suggestions

Hello, I'm a college senior physics student and I don't know how credible I am, so I just wish to make a suggestion/delegate prospective changes. I think RNA folding should either have it's own page, or at least be mentioned as it's own section---titled 'co-transcriptional RNA Folding'. RNA folds on itself in many of the same ways as proteins, where it's partially charged H-bonding bases coulombically pair off in a selective random walk into a least energy configuration, where there is the least energy freely available to contribute to the initiation of conformational changes into other energy configurations, meaning that it's configuration is most stable and least likely to change. The location, order and orientation of folds form motifs that can connect with other motifs to form more complex structures, and then those structures can coulombically bind to complementary (oppositely charged) bonding sites of other structures to form more complex origami (secondary/2D, tertiary/3D, and quaternary/modular structures) (see RNA origami and TectoRNA). The mechanism for RNA folding is often facilitated/chaperoned by protein complexes, such as with RNA polymerase where RNA strands---in Brownian motion---fold while being ejected at variable speed from RNA polymerase during transcription. RNA folding is important because the amino acids that connect into chains---which fold into protein constructs---are carried by-, electrostatically coded for/ordered by-, and assembled into chains by- the various classes of RNA strands & folded RNA origami, and this is done in tandem with protein complexes involved in gene expression and protein synthesis. I think mentioning RNA folding carries a lot of importance because RNA origami looks like it could play a significant role in the future of in vivo nanotechnology. I also think it's worth referencing "Non-covalent interaction" more often when explaining the physics of folding. I also think "Molecular self-assembly" should be referenced, as well as "Supramolecular assembly". And gifs would be ideal, a gif that shows (from left to right) 1) free floating amino acids being picked up by folded tRNA aptamers, 2) carried into a protein/rRNA chaperon---thats anchored to mRNA strand at a position that's electrostatically targeted by rRNA housed within the protein structure---, 3) then bonded to a compatible site on the mRNA strand coding for the amino acid sequence, 4) where the carried amino acid is simultaneously peptide-bonded to the preceding amino acid and released from the tRNA aptamer, then the growing chain of amino acids, while subject to brownian motion, starts folding non-covalently into a protein and then from here we zoom out and follow the little proteins journey from adolescence into it's brutal, bloody, graphic demise in the protease grinder. BiophysicsGuy (talk) 00:51, 5 May 2020 (UTC)

protein NMR spectroscopy

hello sir @My very best wishes:,

can you please review this edit especially the second paragraph, it contains a lot of unclear statements such as:

• Because Protein folding takes place in about 50 to 3000 s−1 (does it mean: 5x10^-1 to 3x 10^-3 second? i couldn't find this numbers in the source.)
• By looking at Relaxation dispersion plots the data collect information on the thermodynamics and kinetics between the excited and ground? (rephrasing would be nice.)
• NOE is especially useful because magnetization transfers can be observed between spatially proximal hydrogens are observed.

thank you.--Momas (talk) 17:28, 30 December 2020 (UTC)

Well, using NMR spectroscopy to study protein folding is enormous subject; one would need a hundred WP pages. As Kozma Prutkov said, "One can not grasp the immensity". You are welcome to contribute. The cited review articles are good. My very best wishes (talk) 01:49, 31 December 2020 (UTC)