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HOW MANY PROTEIN FOLDS there are is a measure of protein family structural diversity and ingenuity. This deck discusses the issues of massive redundancy in curated databanks, problems with definitions, and ways of determining the true number. Another world. https://lnkd.in/emfAhwU View in LinkedIn

COMPLEXITY FROM SIMPLICITY. "The conclusion from all of these coarse-graining approaches is that a reduced alphabet of amino acids is quite capable of producing all protein folds (approx. a few thousand discrete folds) and providing a scaffold capable of supporting all protein functions." https://lnkd.in/eyPrQUq View in LinkedIn

ENZYMES AND SUBSTRATES. "There is an often-surprising size difference between an enzyme and the substrates it works on. For example, in metabolic pathways, the substrates are metabolites which usually have a mass of less than 500 Da while the corresponding enzymes are usually about 100 times heavier." http://book.bionumbers.org/how-big-is-the-average-protein/ View in LinkedIn

VAST NUMBERS. "A typical estimate of the size of sequence space is 20(100) (approx. 10(130)) for a protein of 100 amino acids in which any of the normally occurring 20 amino acids can be found. This number is indeed gigantic but it is likely to be a significant overestimate of the size of protein sequence space." https://lnkd.in/eyPrQUq View in LinkedIn

THE BIG QUESTIONS. "How many protein sequences are there? How many sequences are novel vs. repetitious? How many sequences are characterized at structural and functional levels? Are sequences of prokaryotes, eukaryotes, and viruses different? Is the number of sequence families saturating or is it still expanding rapidly?" https://lnkd.in/evmEhB5 View in LinkedIn

"PROTEIN SEQUENCE SPACE is often viewed as a limitless desert of maladjusted sequences with only a few oases of working sequences linked by narrow pathways. The navigation over this space by natural selection is difficult and could take many different routes thus resulting in organisms with largely different protein compositions." https://lnkd.in/eyPrQUq View in LinkedIn

CURATED PROTEINS. "Now, there are almost 8 million sequences in a nonredundant (NR) database of protein sequences, including the complete genomes of ≈1,800 different species. This large body of data is doubling in size every 28 months." https://lnkd.in/evmEhB5 View in LinkedIn

ASSUMPTIONS. "Two assumptions are generally made when considering the molecular evolution of functional proteins during the history of life on Earth. Firstly, the size of protein sequence space, i.e., the number of possible amino acid sequences, is astronomically large and, secondly, that only an infinitesimally small portion has been explored during the course of life on Earth." https://lnkd.in/eyPrQUq View in LinkedIn

ANSWER: "It's fairly safe to assume that biodiversity can serve as a reliable proxy for protein levels, since abiotic processes that produce proteins are very rare (only happens in submarine hydrothermal vents, if anywhere). If the assumption holds, then the number of proteins has been increasing since the appearance of life 4 - 3.9 billion years ago, experiencing a huge jump 2.3 - 2 Ga with the development of photosynthesis and in the Great Oxidation Event, both of which led directly to an increase in the complexity of life." https://lnkd.in/e25WaJr View in LinkedIn

QUESTION: "How has the total number of proteins on Earth changed over the last few billion years, and how will it change in the future?" https://lnkd.in/e25WaJr View in LinkedIn