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Extra resources for Cell Physiology Source Book. A Molecular Approach
0 ~. Only x-rays have this range of wavelengths. Once a diffraction pattern has been obtained, the problem is to relate the positions of the atoms to one another from the diffraction pattern. The relative positions of two atoms can be computed from their (diffraction) amplitudes and a phase factor that is related to the angular displacement of one atom relative to the other. This phase factor cannot be determined from the diffraction pattern. Since the position of at least one atom is required, in the x-ray diffraction of proteins, a heavy atom bound to the protein is used in the so-called heavy atom replacement method.
D. Possible Interactions between Amino Acids in a Protein Chain As might be expected from the differing nature of the side chains of the naturally occurring amino acids, a vast number of possible interactions between different side chains and backbone are possible for given amino acid sequences. These types of interactions include electrostatic interactions (given by the Coulombic potential qlq2/DR12, where the qs are the charges on two different interacting atoms, R is the distance between them, and D is the dielectric constant of the medium) between positive and negative charges of oppositely charged side chains, such as t h e - C O 0 - group of glutamic acid and the-NH~ group of lysine as well as the interactions between the partial charges on all of the atoms of the protein; n o n b o n d e d interactions between the individual atoms, explained below; hydrogen-bonding interactions between polar atoms with H atoms and other polar atoms; and a soivation energy for most proteins.
T w o - D i m e n s i o n a l High-Resolution N u c l e a r M a g n e t i c R e s o n a n c e S p e c t r o s c o p y (NMR) 60 40 I ~-sheet 20 "random coil" In one of the most exciting developments in protein chemistry, this technique is being applied to solving the structure of proteins in solution without requiring them to be oriented in a crystal. NMR is based on the principle that most nuclei of atoms have spins. If a magnetic field is applied to the atom, the nuclei tend to align their spins with the field.