After formation, proteins spontaneously rotate around single bonds, under electric forces, to make three-dimensional structures {protein folding}|.
process: forces
Amino-acid side chains have polarity. Amino acids can be more polarized, dissolve in water, and tend to be at protein surface. Electric forces are greatest at protein surface, where water interacts with amino-acid side chains. Protein ends polarize and are always at protein surface.
Amino acids can be non-polar and tend to be in protein interior. Protein middle has no water, and side chains there interact among themselves.
process: time
It takes 0.2 second to fold protein.
process: misfolding
One-third of proteins misfold {misfolding, protein}. Rotenone pesticide increases misfolding.
structure
In protein structure, all torques equal zero, and all angular accelerations equal zero. Peptide bonds have no rotation. Typically, all amino acids contribute to structure.
structure: globular
Protein typically becomes globular, because amino-acid chain folds back on itself. Globular proteins have 3.5 to 7.5 loops, with 16 to 24 amino acids each. Loop almost touches ends. Loop goes in same direction as alpha helix coil. Loop follows right-hand rule, with loop going around fingers and thumb in forward-motion direction along sequence.
structure: peptide bond
Peptide bond has N[H2]-Calpha[HR]-Ccarboxy[O]-N[H]-Calpha[HR]-Ccarboxy[O] (2 is subscript).
Bond lengths are the following. C-C for sp^3 = 0.1524 nanometers. C-H for sp^3 = 0.1090 nanometers. C-S = 0.1810 nanometers. S-S = 0.2036 nanometers. C-O peptide bond = 0.123 nanometers. N-H peptide bond = 0.100 nm. Calpha-N = 0.146 nanometers. Calpha-Csidechain = 0.153 nanometers. Calpha-Hsidechain = 0.100 nanometers. Calpha-Ccarboxy = 0.152 nanometers. C-N peptide bond = 0.132 nanometers. Ccarboxy-Cnextalpha = 0.243 nanometers. N-Cnextcarboxy = 0.246 nanometers. Calpha-Nnext = 0.241 nanometers. Ccarboxy-Cnextcarboxy = 0.372 nanometers. N-Nnext = 0.368 nanometers. Calpha-Cnextalpha = 0.381 nanometer.
Bond angles in degrees are the following. C-C-C for sp^3 = 113.0, C-C-H for sp^3 = 109.3, H-C-H for sp^3 = 107.2, C-S-C = 100.4, and C-S-S = 104.5.
Distance between alpha carbons can be 0.381 nanometers {beta sheet, protein}, 0.250 nanometers {alpha helix, protein}, 0.090 nanometers {beta turn, protein}, or random {random coil, protein}.
Protein structure descriptions can use phi angle around N-Calpha axis and psi angle around Calpha-C axis, at all Calphas. One angle has highest probability.
Right-handed alpha helix has phi angle = -57 degrees and psi angle = -47 degrees. Range can be -180 to +180 degrees. Normal range is -180 to +60 degrees. -120 degrees is normal. For proline, angle is always 0 or 110 degrees.
Beta sheet has phi angle -120 and psi angle +120. Range can be -180 to +180 degrees. Normal range is -60 to +120 degrees. Normal is 0 degrees.
technique
To study protein folding, place start position for first amino acid nonexistent alpha carbon at 0,0,0. Pick phi angle. Make new k-axis vector be N-Calpha bond. New i-axis direction is from k-axis line to Ccarboxy. j axis is cross product of k with i. Pick psi angle. Make k-axis vector be Calpha-Ccarboxy bond. New i axis is direction from bond to previous N. j axis is cross product of k with i.
Translate polar coordinates to Cartesian coordinates as necessary. Use many known structures to get actual side-chain coordinates from actual values. Use these to find conditional probabilities for amino acids and nearest, second nearest, and so on, amino acid, to make large table. Do not use alpha helix, beta sheet, or beta turn for values. Just find best parameter set and number.
Physical Sciences>Chemistry>Biochemistry>Protein>Chemical Reaction
5-Chemistry-Biochemistry-Protein-Chemical Reaction
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Date Modified: 2022.0224