Publisher Summary This chapter investigates the anatomy and taxonomy of protein structures. A protein is a polypeptide chain made up of amino acid residues linked together in a definite sequence. Amino acids are “handed,” and naturally occurring proteins contain only L-amino acids. A simple mnemonic for that purpose is the “corncrib.” The sequence of side chains determines all that is unique about a particular protein, including its biological function and its specific three-dimensional structure. The major possible routes to knowledge of three-dimensional protein structure are prediction from the amino acid sequence and analysis of spectroscopic measurements such as circular dichroism, laser Raman spectroscopy, and nuclear magnetic resonance. The analysis and discussion of protein structure is based on the results of three-dimensional X-ray crystallography of globular proteins. The basic elements of protein structures are discussed. The most useful level at which protein structures are to be categorized is the domain, as there are many cases of multiple-domain proteins in which each separate domain resembles other entire smaller proteins. The simplest type of stable protein structure consists of polypeptide backbone wrapped more or less uniformly around the outside of a single hydrophobic core. The outline of the taxonomy is also provided in the chapter.

The anatomy and taxonomy of protein structure.

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme.

(1981). The Internal Dynamics of Globular Protein. Critical Reviews in Biochemistry: Vol. 9, No. 4, pp. 293-349.

The internal dynamics of globular proteins.

Publisher Summary This chapter discusses the biological effects of microwaves. It is emphasized that an appropriate discussion of the experimental results with regard to nonthermal effects must frequently consider thermal effects as well. The amount of energy transfer from the radiation to the material varies slowly with frequency and is largely governed by the dielectric loss. Within reasonable limits, this loss is proportional to the intensity of the radiation. Nonthermal effects, on the other hand, occur in certain frequency regions only, and usually exhibit saturation at rather low intensity. As a consequence, nonthermal effects might be drowned by the thermal ones. This is in particular to be expected when the sign of the considered effect in the nonthermal region is opposite to that of the thermal effect. As an example, consider the reduction of the rate of growth of certain bacteria arising from irradiation at 73.6 Hz as discussed. Temperature increase, on the other hand, increases the rate of growth, thus canceling the nonthermal effect at sufficiently high intensity.

The Biological Effects of Microwaves and Related Questions

A COMPLETE description of an enzyme requires a knowledge of its structure and the dynamics of its function. From the crystal structures of enzymes and enzyme–inhibitor complexes and the known chemistry of model systems, it has been possible in some cases to draw reasonable inferences concerning the mechanisms of enzyme-catalysed reactions. Little has been done so far, however, to supplement such essentially static results by an investigation of the reaction dynamics. This requires an understanding of the internal motions of the enzyme, as well as those of the substrate, since both are likely to be essential to the function. Here we present a theoretical study of a low frequency vibration involving the two globular lobes of lysozyme between which the cleft containing the active site is located1. Any motion involving this cleft could play a part in the catalytic activity; in fact, atom displacements of up to 0.75 A found in a comparison of the free enzyme and the enzyme-inhibitor complex indicate that the cleft has closed down in the latter2. The force constant for the low frequency bending vibration corresponding to the opening and closing of the cleft is obtained from empirical energy functions3. Because the protein surface moves appreciably during the vibration, damping effects resulting from the viscous dissipation in the solvent are included in the calculation4,5.

The hinge-bending mode in lysozyme

Synopsis New techniques in laser Raman spectroscopy are used to obtain spectra of aqueous solutions of lysozyme for frequency shifts as small as 5 ern-'. In addition, Raman measurements are made on two crystalline forms of hen egg white lysozyme. The spectra obtained from the solution and from the crystal are found to be similar for frequencies above 100 cm-'. However, a low-frequency band at 25 cm-' observed in crystalline lysozyme is not found in the solution, indicating that this band cannot be attributed to an internal molecular vibration.

H. Frohlich

Papers

Low-frequency Raman spectra of lysozyme.