Latest from the Protein Folding Field
boscoh.comI link to Boscoh.com, a structural bioinformatician/blogger. He explains of his opinion on the greatest paper in the protein folding field of 2011:
Protein 3D Structure Computed from Evolutionary Sequence Variationthere, that’s in a big enough font. I can’t say I understand this in the slightest, but I believe the basic gist is that Marks et al. have shown from a multiple sequence alignment they can calculate a low resolution protein structure with good confidence. This opens doors to allow structure prediction with low computing costs.
I hope to learn more about the significance of these findings in the future
F1F0 ATP synthase from The Cell
cellimagelibrary.orgGreat animation
“The F1F0 ATP synthase is a large protein complex that catalyzes the formation of ATP from ADP and inorganic phosphate using a proton gradient as a source of energy. In eukaryotes, the F1F0 ATP synthase is found in the inner mitochondrial membrane of the mitochondria and the thylakoid membrane of chloroplasts, and is the primary source of ATP in nearly all organisms. ATP synthase is a multisubunit complex composed of a membrane-embedded F0 portion and a catalytic F1 portion that protrudes above the membrane. The F1 portion is made up of a hexamer of alternating alpha and beta subunits arranged around a core gamma subunit. The F0 portion also consists of several different subunit types, named a, b and c. The c-subunit forms a ring which is in close contact with the gamma subunit of F1. As protons move through the F0 portion, the c-ring rotates, causing the rotation of the gamma subunit within the alpha/beta hexamer. This in turn causes the three nucleotide binding sites in F1 to cycle through different conformations, ultimately leading to the synthesis of ATP. Under the right conditions, ATP synthase can be made to run backwards. In this case, the enzyme will hydrolyze ATP in order to create a proton gradient, and the enzyme is called an ATPase rather than an ATP synthase. In this animation, the hydrolysis of ATP into ADP and inorganic phosphate is illustrated, focusing on the positions of side chains around the nucleotide binding site.”
Crystal Structure of the Activated β-Adrenergic Receptor-Gsα Complex
nature.comG-Protein Coupled Receptors (GPCRs) are integral membrane proteins that receive extracellular signals from the environment and transduce that signal to cause an effect within the cell. There are hundreds of different GPCRs, comprising of about 4% of the human genome. While there is a lot that is understood about how GPCRs work, the actual structure of an activated GPCR-G protein complex has never been solved, due to the difficulty of crystallization. Until now…
I just had a thought.
In structural biology, which is the study of the structures biological molecules take on, it is spectroscopy that holds a magnifying glass. Spectroscopy uses lasers, infrared, magnets, and many wonderfully huge and amazing instruments to poke and prod atoms and the bonds between. Basically, it’s work with resonance frequencies. What are resonance frequencies? Specific, consistent vibrations, like when you push a “C” piano key, it makes a specific tone. So I was thinking… when I use these instruments to knock the electrons around, magnetize atomic nuclei, and basically shake these biological structures to their most essential core…
they talk back to me. They’re whispering back to me what they are. Each bond, each pairing, each little piece has its own small voice and it whispers back to me.
It’s my job to listen.
