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.

Prediction of the secondary structure of proteins from their amino acid sequence.

Publisher Summary In the proper environment, a polypeptide chain can fold spontaneously to the three-dimensional structure of a native protein, and despite the possible presence of barriers in conformational space, the chain can find its way around these barriers to reach the structure of lowest free energy. This chapter describes the spontaneous folding of proteins; in vitro complementation of protein fragments; flexibility of proteins in solution: effect of cross-links and ligands, synthetic analogs of proteins; experimental approaches to the study of conformation; and energetic factors determining protein folding. The interatomic interactions within the chain and between the chain and the solvent dictate the folding and the range of the forces involved, is such that near-neighbor interactions are dominant. Folding is envisaged as taking place by the formation of nucleation sites in various parts of the chain, in response to near-neighbor interactions; the various nucleation sites become stabilized, when they are brought into proximity, so that long-range interactions can become operative. However, the development of conformational energy calculation procedures will enable the three-dimensional structure of a native protein to be predicted from the knowledge of its amino acid sequence and its interactions with the solvent in which it is dissolved.

Experimental and theoretical aspects of protein folding.

Ferricytochrome c: I. GENERAL FEATURES OF THE HORSE AND BONITO PROTEINS AT 2.8 A RESOLUTION

The protein composition of CNS myelin is relatively simple, with two protein fractions comprising 60–80% of the total membrane protein. These are the highly basic, histonelike protein (a single protein in most animals, two in some species) and the hydrophobic proteolipid protein fraction (predominantly a single protein). The remainder of the proteins fall into a heterogeneous group composed of some enzymes, glycoproteins, and an as yet undetermined number of minor proteins of unknown structure and function, most of which have a higher molecular weight than the two major protein fractions. These protein classes are readily separated in several different polyacrylamide electrophoretic systems. The most commonly used procedure is one which employs sodium dodecyl sulfate (SDS) and a high concentration of acrylamide. A typical separation pattern is presented in Fig. 1. The relative proportions and absolute amounts of each protein class can be determined by a spectrophotometric scan of stained or of unstained gels (Greenfield et al., 1971; Poduslo and Braun, 1975).

Proteins of Myelin

The Zimm-Bragg formulation for the one-dimensional Ising model is applied to denatured proteins in order to compute helix probability profiles with different σ and s parameters for the various amino acids; the latter are in principle determinable from melting curves for helix-coil transitions in random copolymers of amino acids. Using a tentative assignment of σ and s values, we found a correlation for the propensity of a residue to be helical in the denatured protein and its occurrence in a helical region in the globular structure of the corresponding native protein. Thus, these incipient helical regions in the denatured chain may serve to nucleate the folding to form the native protein. Short-range interactions appear to determine the tendency for a residue to be helical or not, whereas long-range interactions may serve to carry out the nucleation and refolding processes.

https://www.pnas.org/content/pnas/65/4/810.full.pdf

Helix Probability Profiles of Denatured Proteins and Their Correlation with Native Structures

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Helix Probability Profiles of Denatured Proteins and Their Correlation with Native Structures