Podcast #128: We chat with Kent C Dodds about why he loves React and discuss what life was like in the dark days before Git. Listen now.
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Overview Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures. How do you know when you get it right? Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring a ...


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These are completely different concepts, which sometimes may be connected. A motif in biology is a mathematical model, typically of a sequence, that predicts which sequences belong to some defined group. For example, a DNA sequence motif can characterize the binding site of a transcription factor, i.e. which sequences tend to be bound by this factor. For ...


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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 will be destroyed. If this is happening too often and the amount of chaperones drops too low or the number of unfolded or incorrectly folded proteins becomes ...


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The main problem is that Mad Cow disease is not caused by a "normal" pathogen but by a prion, a protein. Traditionally, disease causing agents can be classified into viruses, bacteria, fungi, and parasites. Bacteria, fungi and parasites are all living organisms, alive in the traditional sense. It is, therefore, possible to design drugs that kill them. ...


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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, showing the ribbon, is from the classic text (long out of print) The Structure and Action of Proteins by Dickerson and Geis. This turns out to be very rare in ...


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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 False Premise “it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids” (My emphasis.) No… What is ...


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in silico modelling of anything in biology is an active field of research. It's very useful for making predictions and developing hypotheses, but any findings need to be confirmed experimentally. From the Folding@Home website: Folding@home has been a success. In 2000-2001, we folded several small and fast folding proteins with experimental validation ...


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Hsp70 and Hsp90 are not single proteins, but entire protein families. And those two protein families are not the only ones of their kind. There are different groups of heat shock proteins, Hsp70 and Hsp90 are molecular chaperones that assist in protein folding. There are five major families of molecular chaperones: Hsp100, Hsp90, Hsp70, Hsp60 and Hsps. ...


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It sounds like your question is "what are the rules to protein folding?" That's not the only way to read your question. Protein Folding is a unique problem - a 1D sequence maps to a 3D object. Since proteins mediate nearly all biochemical transformations and therefore mediate life's processes, protein folding one of the great unsolved problems in ...


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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 a statistical relation where presence of certain amino acids in particular sequences makes one conformation or the other more likely. For example, alanine, ...


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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 interactions in myosin head during powerstroke cycle are not yet known. The only thing we definitely know about how release of Pi from myosin causes ...


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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 protein folding and what proportion of possible sequences gives a working protein. It turns out random sequences are not that likely to fold, which leads to ...


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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 altitudes. Pressure is more of a factor on proteins, and it has been studies very much, both for protein shape and protein interaction with elements and other ...


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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 (called Co-Translational protein folding). Here is the link to an article for basic understanding of co-translational protein folding. There is a lot of debate on ...


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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 was given by Prusiner (1982): Because the novel properties of the scrapie agent distinguish it from viruses, plasmids, and viroids, a new term "prion" is ...


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1) Is the attachment of zinc regarded as a type of post-translational modification? It is not really considered a post-translational modification because the zinc atom is not covalently bound to the protein. Binding to zinc is adsorption. 2) When carbonic anhydrase is denatured, is the zinc ion released in the medium? Yes, but it depends on the ...


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Disclaimer: This is an interesting question if I have understood what you are trying to ask. But unfortunately the case is that there are so many different cases its impossible to cover them here. Other answers talk about folding and modification, but these are still heavily dependant on the "2d" DNA sequence and aren't useful if all one has is a final ...


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One of the quickest ways to get oriented on what is going in the world of protein folding and modeling is to look at the proceedings of the Critical Assessment of Structure Prediction (CASP). CASP is basically a contest, held every 2 years where anyone can use their algorithm to predict the 3D structure of a protein whose structure is known, but not ...


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The answer is more like "It depends on the protein, and the renaturation (or refolding) process." There are a lot of factors that contribute to an individual protein's ability to refold, including size, sequence, secondary structure, amount and type of inter-amino acid links like disulfide bonds, number of subunits, the presence of chaperones/heat shock ...


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Often cells have multiple types of the same protein — this redundancy can have different effects for different requirements such as having proteins function under different physiological conditions, or providing specificity to a certain class of ligand proteins or so on. But here, it seems like the two have some synergistic interaction, a tag team if you ...


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If the process of evolution is driven by completely random process... It's not. The evolution of "better" protein (and other) molecules happens because of selection, a very non-random process. The repeated selection of better molecules, and then of the variants of the better molecules, repeated many times, will lead to "good" molecules (in the sense that ...


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I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper. And the 310 helix was not really right either - it did turn out to show up occasionally in protein structures though. At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal ...


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Substituting a single amino acid and checking the effect this has on a protein is a method to determine what this specific amino acid does in the protein. For example, substituting an amino acid that is part of the catalytic core would almost always make the protein non-functional. Alanine scanning is a technique that methodically replaces amino acids in a ...


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Are multi-chain proteins synthesized as one biological unit? Sometimes yes but mostly not. Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this (See ...


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Preamble In the comments @CMosychuk linked the most comprehensive text on ab initio I have seen this side of the year 2000 (Lee et al., 2009). It agrees that you've raised a good point. It is important to acknowledge that ab initio prediction methods solely based on the physicochemical principles of interaction are currently far behind, in terms of ...


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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 et al. Cell 1993).


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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 has 13 atoms in the ring formed by the hydrogen bond and so can also be called a 3.6-13 helix. The 3-10 helix is less common than the α-helix, but is ...


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