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Proteins and charges are a subtle and complex subject. The most basic answer is that some of the residues (the side chains of the amino acids) are charged. Specifically, aspartic acid and glutamic acid have a negative charge as the word 'acid' suggests and lysine and arginine have a positive charge. Some of the other residues can carry partial charges or dipole moments - one of the atoms in the residue attracts bonding electrons more than other atoms (that is, it's more electronegative) so the atom which attracts bonding electrons more strongly ends up with a partial negative charge and the one which attracts electrons less strongly ends up with a partial positive charge. These full and partial charges can change the charge distribution in nearby residues. If a full or partial negative charge is in close proximity to another molecule's electron cloud, the negative charge will repel the electrons in the other molecule's cloud. If a full or partial positive charge gets near an electron cloud, it will attract the electrons in the cloud. Either way, it will distort the electron cloud. This is called a "dipole - induced dipole interaction." When two molecules are close to each other, there are transient differences in the location of electrons in their electron clouds. Sometimes chance has it that all the electrons in the cloud are on one side of the molecule, so you will see a transient dipole. These transient dipoles can induce dipoles in near by molecules, which in turn reenforce the initial distortion of the electron cloud. These are called "induced dipole - induced dipole interactions." That's at that the atomic or local level. At the macro molecular level (considering entire domains or motifs) there are also charges called macrodipoles, where electronegativity over many successive residues (like in an alpha helix) concentrates most of the electrons in the molecular orbital at one end of the structural element and you get a separation of charge over many residues. The summary is, some charge in proteins is due to actual charges on individual residues, but not much. Most of it results from unequal sharing of electrons between bonded atoms and the effects these full and partial charges have on all the other electrons in the molecule. These affects are additive - small and insignificant by themselves but there are many of them. Usually they cancel each other out and provide structural stability to nearby residues, but sometimes add up and form macrodipoles. Wonderful, wonderful question!
An interesting aside, migratory birds have special proteins with very long alpha helices. These helices accumulate such a strong macrodipole that they spin like compasses in the Earth's magnetic field and guide the birds when they migrate. Which is cool.
the last piece of information is wonderful, and the first one is splendid.....thank you very much
Thank you for asking one about proteins. I am a proteins biochemist and it is not often that there are questions in my field!
Extraordinary answer, Blues! I wish i could make this a sticky...