Prediction of protein conformation.

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.

Publisher Summary This chapter deals with the recent developments regarding the description and nature of the conformation of proteins and polypeptides with special reference to the stereochemical aspects of the problem. This chapter considers the parameters that are required for an adequate description of a polypeptide chain. This chapter focuses the attention on what may be called “internal parameters”—that is, those which can be defined in terms of the relationships among atoms or units that form the building blocks of the polypeptide chains. This chapter also provides an account of the mathematical method of utilizing these parameters for calculating the coordinates of all the atoms in a suitable frame of reference, so that all the interatomic distances, and bond angles, can be calculated and their consequences worked out. This chapter observes conformations in amino acids, peptides, polypeptides, and proteins.

Conformation of Polypeptides and Proteins

Fourier transform ir (FTIR) spectra of 21 globular proteins have been obtained at 2 cm−1 resolution from 1600 to 1700 cm−1 in deuterium oxide solution. Fourier self-deconvolution was applied to all spectra, revealing that the amide I band of each protein except casein consists of six to nine components. The components are observed at 11 well-defined frequencies, although all proteins do not exhibit components at every characteristic frequency. The root mean square (RMS) deviation of 124 individual values from the 11 average characteristic frequencies is 1.9 cm−1. The observed components are assigned to helical segments, extended beta-segments, unordered segments, and turns. Segments with similar structures do not necessarily exhibit band components with identical frequencies. For instance, the lower frequency beta-structure band can vary within a range of approximately 15 cm−1. The relative areas of the individual components of the deconvolved spectra were determined by a Gauss–Newton, iterative curve-fitting procedure that assumed Gaussian band envelopes for the deconvolved components. The measured areas were used to estimate the percentage of helix and beta-structure for each of 21 globular proteins. The results are in good general agreement with values derived from x-ray data by Levitt and Greer. The RMS deviation between 22 values (alpha- and beta-content of 11 beta-rich proteins measured by both techniques) is 2.5 percentage points; the maximum absolute deviation is 4 percentage points.

Examination of the secondary structure of proteins by deconvolved FTIR spectra.

The helix, s Applequist, 1963) in which the Zimm-Bragg parameters u and s are defined respectively as the cooperativity factor for helix initiation, and the equi- librium constant for converting a coil residue to a helical ~~~~

Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins.

A three-dimensional X-ray study at a resolution of 2.8 A has revealed that the single polypeptide chain of 211 residues is folded into two distinct parts which are divided by a cleft. The active site, consisting of a cysteine and a histidine, lies at the surface of the cleft. Apart from four short α-helical segments and one short segment of β-structure, the conformation of the chain is irregular.

Structure of papain.

Publisher Summary The fruits of the tropical papaya tree have latex that contains several enzymes. This chapter focuses on two different proteolytic enzymes: chymopapain and papain. Both enzymes belong to the group of proteolytic plant enzymes that require a sulfhydryl group for activity. The chapter discusses the enzymatic properties of papain. Papain can catalyze a number of reaction—namely, acyl-enzyme intermediate, hydrolysis, transferase action, and specificity. X-ray diffraction can provide a wealth of information on a protein structure. The papain molecule consists of one folded polypeptide chain of 212 residues. The sequence determination of these residues is an example of the mutual interaction between purely chemical and X-ray methods. Because of the many difficulties that papain presented to the chemists, only a tentative sequence could be published in 1964. Some of the overlaps were not found to be as conclusive as desired, and at least one gap existed in the sequence. The available information, however, permitted the interpretation of the electron density map. Moreover, the difficulties in the early chemical sequence studies on papain because of the insolubility of the denatured protein and many of its peptides is circumvented by the use of completely carboxymethylated papain that has been fully maleylated.

The structure of papain.

A Comparison of the Three-dimensional Structures of Subtilisin BPN′ and Subtilisin Novo

The double domain structure of rhodanese

https://www.jstor.org/stable/info/2416936

J.N. Jansonius

Papers

Structure of papain.

The structure of papain.

A Comparison of the Three-dimensional Structures of Subtilisin BPN′ and Subtilisin Novo

The double domain structure of rhodanese

The structure of the papain molecule