Calculation of protein extinction coefficients from amino acid sequence data

Publisher Summary This chapter explores that the changes that take place in the protein molecules during denaturation constitute one of the most interesting and complex classes of reactions that can be found either in nature or in the laboratory These reactions are important because of the information they can provide about the more intimate details of protein structure and function They are also significant because they challenge the chemist with a difficult area for the application of chemical principles The chapter reviews that the denaturation is a process in which the spatial arrangement of the polypeptide chains within the molecule is changed from that typical of the native protein to a more disordered arrangement The chapter also discusses the classification of protein structures: primary, secondary, and tertiary structures The primary structure is that expressed by the structural chemical formula and depends entirely on the chemical valence bonds that the classical organic chemist would write down for the protein molecule The secondary structure is the configuration of the polypeptide chain that results from the satisfaction of the hydrogen bonding potential between the peptide N-H and C=O groups The tertiary structure is the pattern according to which the secondary structures are packed together within the native protein molecule The term “denaturation” as used in this chapter is indented to include changes in both the secondary and tertiary structures

Some factors in the interpretation of protein denaturation.

Publisher Summary This chapter discusses the chemical analysis of microbial cells. The preparation of material for analysis is discussed, because changes in the chemical composition of cells may occur as a result of the washing and storage conditions used. Wet- and dry-weight determinations of bacterial samples and assay of total cell numbers are described, because analytical results must refer to one or other of these values. Selection of an analytical procedure is a subjective process, because the number of suitable methods is large and each will have different merits and defects. Primary considerations are sensitivity, specificity, reproducibility, and absolute accuracy. Automatic methods for performing biochemical analyses, already widely accepted in hospitals and in industry, are beginning to make their way into the research laboratory. All automatic analyzers developed so far may be classified as either “continuous-flow” or “discrete” types. All of them use colorimetric methods exclusively and contain some form of automatic colorimeter for final read-out. The first and best-known is the Technicon “AutoAnalyzer,” which is of the continuous-flow type.

Chapter III Chemical Analysis of Microbial Cells

Publisher Summary This chapter reviews that the simplest way of accounting for the absorption spectrum of a protein is as the sum of the spectra of its components. This gives results which are often good approximations to the observed protein spectrum. The assumption of additivity is basic for useful analytical applications of spectral measurements. It discusses that in another perspective, the failure of perfect additivity of the component absorptivities affords the possibility of obtaining structural information about proteins. The absorptivity of the peptide bond can change by as much as a factor of two with a change in the conformation of a peptide chain. Since the absorptivity of aromatic side chains is much less sensitive to environmental change, correspondingly, more sensitive techniques are required to measure the small changes which do occur. The nature and limitations of the structural information resulting from both peptide-bond and side-chain absorption are discussed. Absorption spectra can occasionally be a useful tool in the identification of unusual structural features in proteins and polypeptides. Several such applications are also explained in this chapter.

Ultraviolet spectra Of Proteins and Amino Acids

Determination of Tyrosine and Tryptophan in Proteins

Publisher Summary This chapter deals with the absorption spectra of proteins and amino acids The colored proteins are conjugated proteins in which the protein carrier is colorless This transparency of protein solutions extends into the ultraviolet region of the spectrum and many proteins do not absorb radiation of longer wavelength than 2500 Ǻ The essential protein fabric, consisting of a peptide chain in various forms, is not responsible for absorption at longer wavelengths In case of fibrous proteins, there is some evidence that the peptide fabric is responsible for absorption in this region Many proteins absorb in this region This absorption is due to the aromatic amino-acids present in the protein The advent of quantitative methods of spectrophotometry is the basis of a method of determining tyrosine and tryptophan in proteins The striking property of proteins is their transparency, indicating a high degree of electronic saturation The configurational stability of the protein molecule depends entirely on extra-valence forces and not on unsaturation, which would result in high absorption in the ultraviolet The absence of such rigidifying bonds endows the protein with its unique characters of plasticity, while the number-sequence of side chains gives its chemical constancy These two properties allow these molecules to be arranged in large polymorphic masses to form a matrix fabric of recurrent pattern in media, which are essentially aqueous The material reviewed is principally derived from the study of homogeneous absorbing systems, in which the inhomogeneity is finer in grade by several orders than the dimensions of the exploring light beam

E R Holiday

Papers

Ultraviolet absorption spectra of proteins and amino acids.