Biological complexity: finding working proteins (Introduction)

by David Turell , Wednesday, October 28, 2015, 23:14 (3100 days ago) @ David Turell

Another article on the rarity of functional proteins:-http://www.evolutionnews.org/2015/10/proteins_by_acc100411.html-"In fact, the vast majority of possible protein chains are like strands of beads -- lacking any fixed shape. Life, however, makes critical use of a very special subset of the possibilities. These special proteins are coaxed into forming precise shapes by the sequence of amino acids along their chains. The process triggered by this coaxing, where a floppy protein chain rapidly acquires a well-formed structure, is known as folding.-"To give you an idea of how special these folding sequences are, the Journal of Molecular Biology paper referred to in the video estimates the proportion of chains that fold to be in the range of one in 10^50 to one in 10^74, depending on the complexity of the fold.-"Even for simple folds, this means fewer than one in a trillion trillion trillion trillion amino acid sequences forms any well-defined shape at all. So the idea that every protein sequence has a shape is not at all accurate.-"Secondly, the related idea that mutations merely change the shapes of proteins is equally inaccurate. The highly cooperative nature of protein folding means that it tends to be all-or-nothing. A particular protein sequence either forms structure A or it doesn't, and likewise for structure B. So for a series of mutations to convert a protein from forming structure A to forming structure B, they would first have to undo the A structure (producing a chain with no well-defined structure) and then stabilize the B structure.-"In other words, changing the structure of a protein isn't nearly as easy as changing the shape of a lump of clay. The clay always has a shape, and with a little imagination we can even say the shape always represents something (which is all we ask of a lump of clay).-"Proteins are different. Only highly exceptional proteins even have a shape, and these shapes are therefore fragile. Mutations are tolerated to a modest extent, after which all shape is lost.-Comment: If mutations are the result of blind searching, based on the odds above, how does evolution find the right proteins for a new adaptation for innovation? There must be DNA guidelines on board or there is not enough time for evolution to fit the timelines we know. Thus the two approaches we discuss: on board guidance or external guidance. There can be nothing else.