The molar absorption coefficient, E, of a protein is usually based on concentrations measured by dry weight, nitrogen, or amino acid analysis. The studies reported here suggest that the Edelhoch method is the best method for measuring E for a protein. (This method is described by Gill and von Hippel [1989, Anal Biochem 182:3193261 and is based on data from Edelhoch [1967, Biochemistry 6:1948-19541.) The absorbance of a protein at 280 nm depends on the content of Trp, Tyr, and cystine (disulfide bonds). The average E values for these chromophores in a sample of 18 well-characterized proteins have been estimated, and the E values in water, propanol, 6 M guanidine hydrochloride (GdnHCI), and 8 M urea have been measured. For Trp, the average E values for the proteins are less than the E values measured in any of the solvents. For Tyr, the average E values for the proteins are intermediate between those measured in 6 M GdnHCl and those measured in propanol. Based on a sample of 116 measured t values for 80 proteins, the t at 280 nm of a folded protein in water, t(280), can best be predicted with this equation:

https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.5560041120

How to measure and predict the molar absorption coefficient of a protein.

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

/pdf/dominant-forces-in-protein-folding-42bjzlldw4.pdf

Dominant forces in protein folding

Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that measurements may be made on multiple samples containing < or =20 microg of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.

/pdf/using-circular-dichroism-spectra-to-estimate-protein-3jces2e55y.pdf

Using circular dichroism spectra to estimate protein secondary structure

Chain Structure and Configuration. Molecular Weights and Sizes. Concentrated Solutions and Phase Separation Behavior. The Amorphous State. The Crystalline State. Polymers in the Liquid Crystalline State. Glass-Rubber Transition Behavior. Cross-Linked Polymers and Rubber Elasticity. Polymer Viscoelasticity and Rheology. Mechanical Behavior of Polymers. Modern Topics. Index.

http://toptop.persiangig.com/sperling/12.pdf

Introduction to physical polymer science

NMR Studies of Cyclodextrins and Cyclodextrin Complexes

The free electron model of Pauling is used to calculate the magnetic field around a benzene ring which is rotating rapidly about all axes in an external magnetic field. It is assumed that the π electrons precess in two circular paths, one on each side of the ring, equal in radius to the C–C distance in the benzene ring. The separation of these rings is taken as 1.28 A, which gives a calculated value for the nuclear magnetic resonance shielding value for benzene protons equal to the observed value. The field thus calculated is employed to predict shielding values for other aromatic compounds. Agreement with experiment is in general good, but there are some exceptions.

Calculation of Nuclear Magnetic Resonance Spectra of Aromatic Hydrocarbons

High resolution NMR of macromolecules

Spectra of methyl methacrylate polymers in chlorofornm solution at 90° show three α-methyl proton peaks. Measurements of their areas in spectra of polymers prepared with free radical and anionic initiators indicate that these may be attributed to (1) iso- tactic sequences (ddd or lll), (2) syndiotactic sequences (ldl or dld), and (3) heterotactic sequences (ldd, dll, ddl, or lld). The conformation and stereochemical configuration of the chains may thus be examined with considerable discrimination; degrees of regularity. block sizes, etc. appear to be determinable. Free radical polymers of methyl methacrylate are found to be predominantly syndiotactic, whereas those produced with anionic initiators. such as n-butyllithium, are shown to be predominantly isotactic, in agreement with the findings of others. The backbone methylene resonance also shows striking changes with chain stereochemical configuration, such as to provide absolute, independent confirmation of the assigned structures.

Polymer NSR spectroscopy. II. The high resolution spectra of methyl methacrylate polymers prepared with free radical and anionic initiators

Preface. Fundamentals of Nuclear Magnetic Resonance: Introduction. Nuclear Spin and the NMR Phenomenon. Detection of the Resonance Phenomenon. Nuclear Relaxation. Magnetic Shielding and the Chemical Shift. Indirect Coupling of Nuclear Spins. Rate Phenomena: Averaging of Chemical Shifts and JCouplings. Experimental Methods. The Microstructure of Polymer Chains: Introduction. Polymer Microstructure. Configurational Statistics and Propagation Mechanism. Propagation Errors. The Solution Characterization of Polymers: Introduction. Resonances Assignments. Microstructural Characterization of Polymers in Solution. The Solution Structure of Polymers. The Solid-State NMR of Polymers: Introduction. Chain Conformation in the Solid State. The Organization of Polymers in the Solid-State. NMR Imaging of Polymers. The Dynamics of Macromolecules: Introduction. Polymer Dynamics in Solution. Polymer Dynamics in the Solid State. Subject Index.

Frank A. Bovey

Papers

Calculation of Nuclear Magnetic Resonance Spectra of Aromatic Hydrocarbons

High resolution NMR of macromolecules

Polymer NSR spectroscopy. II. The high resolution spectra of methyl methacrylate polymers prepared with free radical and anionic initiators

NMR of polymers

Interpretation of the ultraviolet spectral changes of proteins.