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Sometimes SwissProt annotations come from direct experimental evidence, but this is rare. It depends on the entry, but more often than not the annotation will have been obtained by some kind of sequence analysis or prediction based on sequence similarity.


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Interactions denote protein-protein interactions, which means physical association between proteins. By nature, these networks/graphs are undirected. Replication interactions (actually a not very good term) denote gene regulatory interactions that affect HIV replication. These sets also include the regulatory effects of HIV genes on host genes (and hence ...


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I want to add a book to the list that may be easier for you since it takes it from the perspective of Physics: Finkelstein & Ptitsyn, Protein Physics, Academic Press (2002). ISBN 0-12-256781-1. It covers structure, thermodynamical processes in proteins, mechanism of folding, function, a bit of bioinformatics. It is designed as a master level course in ...


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This has been studied by some of my labmates in Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? I am not involved in their research, but here is the gist of the paper: Different scales are, as you say, developed based on different criteria. In particular, Eisenberg scale is one of the consensus ...


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Given your background (not a biologist or chemist) you would probably find the introductory material in a biochemistry "lite" textbook more accessible/useful than a hardcore text for specialists. As a co-author of a biochemistry textbook, I can tell you that there are essentially three different classes, or types of texts. Comprehensive textbooks, of ...


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The secretion pushes the cell organelles to the basal part. (although the fat cells have no polarity, their organelles have been pushed to one side of the cell: Comparing to adipose cells, the acinar cells secrete their specific proteins on one specific end of the cell, this is why in contrast with fat cells they have well defined polarity.


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Cooking is just a form of digestion. What is digestion? Digestion is the process of breaking down big molecules into smaller molecules. When you cook food you break down big molecules into its small components. Why do we digest food? Think about a long sequence of DNA for example. You eat corn and you have in your body a long sequence of corn ...


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The best way is to use FPLC if you know what kind of protein you're looking for.in case you don't know what are you looking for,then you can run a 2D-PAGE and after analyzing spots then use LC MS/MS to identify your proteins and then continue with FPLC ( for record FPLC is a method of HPLC or LC which is protein friendly and even you can use it to isolate ...


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Although quantitative methods using MS have been developed, MS is not inherently quantitative. Quantification with MS could be quite tricky. Therefore, it is not the first choice. But, if you do not know which protein levels change and want to find proteins the expression levels of which are different between your samples you are going to compare, MS is not ...


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Western blot, though is a commonly used technique and is relatively simple to do, has some issues: Low throughput: it is difficult to analyse multiple proteins simultaneously Limited cross comparability: since antibodies to different proteins can have different affinities, they cannot be compared with each other. Low sensitivity Not very quantitative ...


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You will probably want to read up on Position Frequency Matrices (PFMs) and Position Weight Matrices (PWMs). These tend to be much more sensitive and useful for pattern recognition in nuclei acid sequences. Two examples of databases with these patterns are TRANSFAC and JASPAR. Regex patterns can be useful in protein sequences sometimes, although PWM have ...


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Prosite (http://prosite.expasy.org/) uses regular expressions to search for protein domains, in contrast with Pfam. If you look at an entry, such as http://prosite.expasy.org/cgi-bin/prosite/prosite-search-ac?PDOC00022, you can see the consensus pattern under the PATTERN section towards the bottom. Prosite does not have the same coverage as Pfam, but the ...


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Regular expressions are not commonly used for DNA or Protein analysis, but many people use Hidden-Markov-Models (HMMs). If you are looking at protein domains, you can find many HMMs here: http://pfam.xfam.org/


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Your question is answered in the paper, the protein likely exists as a homodimer in vivo and denaturation (such as performed with SDS PAGE -> Western Blot) separates the dimers into monomers: "To determine the quaternary structure, size exclusion high-performance liquid chromatography was performed using an Agilent 1100 series high-performance liquid ...


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With a few exceptions among some bacteria, all species on the planet make protein from the same 21 amino acids, and the relative abundances of amino acids is very similar in proteins from plants, animals, fungi and even prokaryotes. See for example this article (available as PDF here). So protein from pretty much any food provides the same amino acids. The ...


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It's because E.coli BL21(DE3) are competent cells. The competent is the key here as the cells were chemically treated so the transfection can be performed by heat-shock with high efficiency. This means these bacteria are quite fragile, due to the chemical treatment, and therefore are very sensitive to both mechanical and thermal shocks. Pre-heating the ...


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Each daughter cell, following mitosis, will contain some ribosomes and DNA transcription machinery already, so it can already synthesise more ribosomes. In the case of the fertilised ovum, when the organism is only a single cell, the first ribosomes will be those already present in the unfertilised ovum. So cells never have to start from scratch with no ...


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From the comment section: Cells divide and when they do the two daughter cells will not only have copies of the DNA but also of the organelles, the cellular machineries and the cell membrane which implies that yes the daughter cells receive also ribosomes. The replication happens during the interphase.



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