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10 votes
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Do chaperone proteins misfold?

Chaperone proteins are still proteins and they can certainly misfold just like any other. If that happens, it will either be assisted by another chaperone and given time to fold successfully or it ...
forest's user avatar
  • 297
9 votes
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What are the different types of helices in protein secondary structures and how do they differ?

This DSSP page makes it clear that: Helix-3 = 3-10 helix Helix-5 = π-helix The α-helix is described in every biochemistry text book and widely on the web. It has 3.6 residues per helical turn and ...
David's user avatar
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8 votes
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Backbone hydrogen bonds between adjacent amino acids in a protein?

The situation you ask about was originally part of the 27 ribbon and 2.27 helix structures considered as possibilities by protein chemists (Linus Pauling?) in the 50s or 60s. The diagram below, ...
David's user avatar
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7 votes
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Difference between prions and amyloid proteins?

Amyloids are protease resistant insoluble fibrils formed because of (mis)folding and aggregation of soluble proteins (Rambaran and Serpell, 2008, Sabate et al., 2015). The first definition of prion ...
WYSIWYG's user avatar
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7 votes

Why is it thought that protein folding is determined solely by amino acid sequence?

This question is, in my opinion, based on an incorrect premise but nevertheless throws up a number of points about protein folding and protein structure that can be addressed, albeit briefly. The ...
David's user avatar
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6 votes
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Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?

Yes, there are certain amino acid sequences that tend to form alpha-helices, and others that prefer to form beta-sheets. There is no perfect correspondence between sequence and structure, but there is ...
Roland's user avatar
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6 votes
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Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales?

I think your acquaintance is trying to fit real science to some of his personal beliefs (that are obviously wrong). If you read the article you'll see that it's not about evolution at all, but about ...
VonBeche's user avatar
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6 votes
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When does protein folding begin?

When does protein folding begin? With reference to time you have asked, it can be after the translation has occurred (called Translational protein folding) or while translation is still occuring (...
Science123's user avatar
6 votes
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If a protein has multiple globular domains with flexible peptide linkers in between, how do they fold?

A broad interpretation of the question The question refers to the “folding” of proteins. This term — and the associated biological problem — is often used in the rather specific sense of the ...
David's user avatar
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5 votes
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Are proteins a different shape in space?

Proteins are not made to be one way up or the other as they flow around and surround cells, so sea-level to space gravity gradient will not be the major cause of change to proteins at different ...
bandybabboon's user avatar
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5 votes
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Mechanism of Myosin Head Bending in Cross Bridge Cycle Power Stroke Phase

Introduction: This is going to be quite a long answer. To have an introduction to the topic, you can have a look at articles from Wikipedia and RCSB Protein Data Bank. The exact mechanism of physical ...
another 'Homo sapien''s user avatar
5 votes
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Proteins in water vs proteins in crystal

Protein crystals are not like crystals of more commonly found substances like salt [NaCl] or diamond [carbon only.] These materials do not include other atoms in their crystal structures. For ...
Edward Kowal's user avatar
5 votes
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What characteristics of the protein folding process ensure that the energy landscape is a funnel?

Naturally occurring proteins are evolved such that this is the case Natural proteins only occupy a very small amount of sequence space. For a 200 aa protein, there are $20^{200} \approx 10^{260}$ ...
R.M.'s user avatar
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5 votes
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Protein structure prediction from amino acids sequence

what is the accuracy we can predict tertiary protein structure That depends on the protein. If the primary sequence closely matches the sequence of a protein for which the structure is already ...
acvill's user avatar
  • 8,326
5 votes

Allowed Deviations in fixed bond length and bond angles in peptides from the typical values

Single-conformation descriptions of the native-state ensemble, under ambient conditions, are expected to have close to ideal geometries. This is a result from Statistical Mechanics; the probability of ...
Ryan's user avatar
  • 1,321
4 votes

Can a bacterium survive without GroEL protein?

In E. coli, GroEL/GroES is found to interact with about 10% of all soluble proteins (Kerner et al. Cell 2005) and is the only chaperone essential to the bacterium under all tested conditions (Horwich ...
ACouce's user avatar
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4 votes
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How can I render a protein non-functional to avoid problem during expression?

Inclusion body (IB) is a technique used to express proteins that are toxic to the host cells. IBs are aggregate of highly similar or the same kind of proteins in the cytoplasm formed as stress ...
Leading Biology's user avatar
4 votes
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Could AI be applied to protein folding?

Yes, and no :-) In the meantime many protein structures can be predicted quite accurately - even those for which no reference fold had been known before. In this case the important buzz word is "...
tsttst's user avatar
  • 1,597
4 votes

How does the shape of a protein determine its function?

Determining function and predicting function are two separate things. For example, a screwdriver's shape determines its function, but it might be hard to predict that function unless you also see some ...
Armand's user avatar
  • 1,721
3 votes

Can estimating the likelihood of protein sequences adopting functional enzyme folds show life is too complex for evolutionary timescales?

Conclusions from the paper. The finally line in the article should actually be read first as it clearly spells out where the paper fits in the scientific literature. So, if re-creating a fold by ...
James's user avatar
  • 11.3k
3 votes
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Why are proteins in the insoluble form when they are in frozen water?

This answer is about cold denaturation of proteins rather than the effect of freezing. The folded structure of a protein is thermodynamically stable as a result of a small favourable difference ...
Alan Boyd's user avatar
  • 22.8k
3 votes

Why are proteins in the insoluble form when they are in frozen water?

If proteins change from being water soluble to water insoluble it means that their three-dimensional structure changed, because this determines how the protein interacts with the water. Most proteins ...
Nicolai's user avatar
  • 4,391
3 votes

What is protein folding and how is it relevant to disease?

Protein folding is a complex thing. There are huge computer algorithms and huge mainframes which are trying to predict the final 3D structure of a protein. Knowing the tertiary and the quaternary ...
flavinsky's user avatar
  • 186
3 votes

Structure of proteins

primary structure focus = peptide bonds (because these link the amino acids The sequence of amino acids, for example AGGVHIL.. secondary structure focus = H-bonds between the parts of the backbone ...
KingBoomie's user avatar
  • 2,390
3 votes
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Thermodynamics of spontaneous protein folding: role of enthalpy changes

Summary The first explanation is commonly encountered. The second explanation cannot be correct, as it stands, as it ignores the free energy change in the protein. A modification of the second ...
David's user avatar
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3 votes
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Relation of conformational entropy and protein folding

This question is an example of an important general problem in chemical biology: “How does an ordered system arise without violating the second law of thermodynamics?” Berg et al., Biochemistry, ...
David's user avatar
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3 votes

What proportion of proteins require chaperone-assisted folding?

I'm reminded of a lovely review in Trends in Biochemical Sciences that discusses chaperone independent, partially dependent, and fully dependent proteins in prokaryotes. The conclusion was that ...
De Novo's user avatar
  • 8,811
3 votes

What does 'kinetically accessible' mean in protein folding?

At some point during protein folding, there may exist lower energy states from a thermodynamic perspective (lower ΔG free enegy) which are actually unreachable in a given environment, because the ...
Eliane B.'s user avatar
  • 1,145
3 votes
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Why does it matter to predict protein structure?

How do you want to predict function and binding partners without knowing how your protein looks like? The sequence itself contains only limited information. Similar sequences might fold into similar ...
Frieke's user avatar
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