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Protein sequencing is a nicely constrained problem: you have a one-dimensional sequence of amino acid members, which come from a limited set of options (made a bit more complicated by post-translational modifications, but not much more so). Because it's one-dimensional, it's a problem you can easily solve by chopping up a protein into little bits, using mass ...


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To answer why sequences are known before structures, it is worth highlighting the typical ‘workflow’ for a biochemical researcher. Briefly, sequence is always before structure because you need the sequence to determine the structure. As with everything else one would like to investigate, you have to start with the information that you already have. In modern ...


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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 resolved, then template-based methods to model 3D structure can be used (a.k.a homology modeling). These methods tend to be accurate, as assessed by template-...


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As mentioned in the comments, diagrams like these are generated by software. The one I use is Chimera, it is free. The structure of the protein is recorded as a list of atoms and their 3D coordinates, as well as bonds, helices, sheets, etc. When a structure file is loaded, the software generates a 3D model based on the data. The user can rotate the model, ...


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This article : Prakash Arumugam, Stephan Gruber, Koichi Tanaka, Christian H. Haering, Karl Mechtler, Kim Nasmyth, "ATP Hydrolysis Is Required for Cohesin's Association with Chromosomes", Current Biology, Volume 13, Issue 22, 2003, at https://www.sciencedirect.com/science/article/pii/S0960982203008042 Their conclusion is: "Conclusions: Cohesin ...


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As described in the abstract of Synthetic Cross-linking of Peptides: Molecular Linchpins for Peptide Cyclization by Derda et al., protein cyclization improves: resistance to proteolytic degradation and conformational stability. The latter property leads to an increase in binding potency and increased bioavailability due to increased permeation through ...


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The predictioncenter.org runs an open contest every two years - Critical Assessment of Structure Prediction (CASP). CASP 14 is underway now. The best programs for ab initio folding are highly augmented molecular dynamics with machine learning and a bunch of predictive algorithms aggregated to create a structure. Look at David Baker's Rosetta software. More ...


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There are various software programs available to design a protein structure based on your requirement. These programs can be used to: Design atomic model based on the amino acid sequence of particular protein. Predicting protein's 3-Dimensional structure. Determining secondary and tertiary structure of protein based on it's protein folding properties and ...


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Sequencing a viral genome requires isolation of the virus, propagation in cell culture, extraction of nucleic acids, and preparation of a sequencing library. Once sequences are obtained, a genome can be assembled de novo using (untargeted) shotgun reads, and gaps in the genome can be spanned with (targeted) Sanger sequencing. This process can take weeks to ...


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Think about the case of a chain of N=3 points in space. There are only angles associated with the middle point, the two endpoints don't have angles associated with them because they only have one incident segment rather than two.


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Firstly protein structures are not infinite. Most proteins adopt specific structure. Drugs carry out their function by binding to its target protein. Structure prediction helps drug discovery process in two ways - it allows identification of pockets in target proteins (where drugs can bind) whose structures are not yet solved using experimental methods it ...


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Sequencing DNA (which is what was done for the COVID virus, post reverse transcription as it is an RNA virus) does not take very long. A NextSeq instrument can provide results in <24 hours. Protein sequences are inferred from the DNA sequence using gene/ORF calling software. SOme of this is suggested by @acvill, though I think that they are pessimistic ...


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I have found this image on Biology LibreTexts, and they have answered my question. Like I suspected, the large residues will mainly project out of the beta pleated sheet and will not interfere much with the backbone hydrogen bonds. In alpha helices, however, the branched and aromatic residues are still able to project into the helix (as they are not pointing ...


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This table is from the Wikipedia page for α-helix: As you can see aromatics are not the worst offenders. In fact, barring proline (whose backbone torsion angles are unsuited to helices), Gly is the worst offender. A likely reason for this is Gly being too flexible i.e. its small side chain H allows it to adopt backbone torsion angles unsuited for α-helix. ...


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There are research groups working on this exact question; understanding cold adaptation in enzymes. You can read about this in several articles such as 'Computation of enzyme cold adaptation', or 'Molecular Structural Basis for the Cold Adaptedness of the Psychrophilic β-Glucosidase BglU in Micrococcus antarcticus', or 'Specific amino acids responsible for ...


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