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A simple method for displaying the hydropathic character of a protein

A rapid DNA isolation procedure for small quantities of fresh leaf tissue

Poly(N-isopropylacrylamide): experiment, theory and application

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.

T e purpose of this review is to assess the nature and magnitudes of the dominant forces in protein folding. Since proteins are only marginally stable at room temperature,’ no type of molecular interaction is unimportant, and even small interactions can contribute significantly (positively or negatively) to stability (Alber, 1989a,b; Matthews, 1987a,b). However, the present review aims to identify only the largest forces that lead to the structural features of globular proteins: their extraordinary compactness, their core of nonpolar residues, and their considerable amounts of internal architecture. This review explores contributions to the free energy of folding arising from electrostatics (classical charge repulsions and ion pairing), hydrogen-bonding and van der Waals interactions, intrinsic propensities, and hydrophobic interactions. An earlier review by Kauzmann (1959) introduced the importance of hydrophobic interactions. His insights were particularly remarkable considering that he did not have the benefit of known protein structures, model studies, high-resolution calorimetry, mutational methods, or force-field or statistical mechanical results. The present review aims to provide a reassessment of the factors important for folding in light of current knowledge. Also considered here are the opposing forces, conformational entropy and electrostatics. The process of protein folding has been known for about 60 years. In 1902, Emil Fischer and Franz Hofmeister independently concluded that proteins were chains of covalently linked amino acids (Haschemeyer & Haschemeyer, 1973) but deeper understanding of protein structure and conformational change was hindered because of the difficulty in finding conditions for solubilization. Chick and Martin (191 1) were the first to discover the process of denaturation and to distinguish it from the process of aggregation. By 1925, the denaturation process was considered to be either hydrolysis of the peptide bond (Wu & Wu, 1925; Anson & Mirsky, 1925) or dehydration of the protein (Robertson, 1918). The view that protein denaturation was an unfolding process was

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Dominant forces in protein folding

Data for ligand and receptor binding presented in the format of a Scatchard graph are compared with the same data shown as bound ligand plotted against the logarithm of free ligand. From this comparison it is apparent that extrapolations in the Scatchard graph to yield total number of receptor sites are generally not correct.

https://science.sciencemag.org/content/sci/217/4566/1247.full.pdf

Numbers of receptor sites from Scatchard graphs: facts and fantasies

Properties of graphical representations of multiple classes of binding sites.

Hydrogen Bonds between Model Peptide Groups in Solution

STOICHIOMETRY OF SUBUNITS. . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 DISSOCIATION METHODS . . . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Denaturants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Change of charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Binding of metabolites or s mall ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Reaction with sulfhydryl groups .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 HyBRIDIZATION .... . . . . . . . . . . . . . . . . . . • . . . . . • • • . • . . . . . • . . . .. .... ... .. . 28 TABLE OF SUBUNITS . . . ' " . . . . . . . . . . . . . . . . . . . . . . . • • . . . . . . . ..... ... . .. . 29 GEOMETRIC ARRANGEMENTS OF SUBUNITS 29 CYCLIC SYMMETRY . . . . . . . . . • • . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 DIHEDRAL SYMMETRY . . . . . . . • . . . . . . . . . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . 36 CUBIC SYMMETRY • • . • . . . . . . • . • . . . . . . . . • . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . 38 GENERAL COMMENTS . . . . . • . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 ENERGETICS OF INTERACTIONS 39 MOLECULAR STRUCTURE OF INTERFACE CONTACTS 52 FACTORS THAT MODIFY SUBUNIT INTERACTIONS S6 INTRINSIC FACTORS . . . . . . . . . . . . . . . . . . . . . . . • . . . . . . . . • . . . . . . . . . . . . . . . . . • 56 EXTRINSIC FACTORS . . . . . . • • . . . . . . • • . . • . . . • . . . . • . . . . . . . . . . . . . . . . . . . . . . . S7 CONCLUSION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S9

Irving M. Klotz

Papers

Numbers of receptor sites from Scatchard graphs: facts and fantasies

Properties of graphical representations of multiple classes of binding sites.

Hydrogen Bonds between Model Peptide Groups in Solution

Quaternary Structure of Proteins

Slow hydrogen-deuterium exchange in a non-.alpha.-helical polyamide