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

We discuss possible motions for one polymer molecule P (of mass M) performing wormlike displacements inside a strongly cross‐linked polymeric gel G. The topological requirement that P cannot intersect any of the chains of G is taken into account by a rigorous procedure: The only motions allowed for the chain are associated with the displacement of certain “defects” along the chain. The main conclusions derived from this model are the following:(a) There are two characteristic times for the chain motion: One of them (Td) is the equilibration time for the defect concentration, and is proportional to M2. The other time (Tr) is the time required for complete renewal of the chain conformation, and is proportional to M3.(b) The over‐all mobility and diffusion coefficients of the chain P are proportional to M−2.(c) At times t < Tr the mean square displacement of one monomer of P increases only like 〈(rt − r0)2〉 = const t1/4.These results may also turn out to be useful for the (more difficult) problem of entangle...

Reptation of a Polymer Chain in the Presence of Fixed Obstacles

The necessary coordination of the motions of different parts of a polymer molecule is made the basis of a theory of the linear viscoelastic properties of dilute solutions of coiling polymers. This is accomplished by use of the concept of the submolecule, a portion of polymer chain long enough for the separation of its ends to approximate a Gaussian probability distribution. The configuration of a submolecule is specified in terms of the vector which corresponds to its end‐to‐end separation. The configuration of a molecule which contains N submolecules is described by the corresponding set of N vectors. The action of a velocity gradient disturbs the distribution of configurations of the polymer molecules away from its equilibrium form, storing free energy in the system. The coordinated thermal motions of the segments cause the configurations to drift toward their equilibrium distribution. The coordination is taken into account by the mathematical requirement that motions of the atom which joins two submolecules change the configurations of both submolecules. By means of an orthogonal transformation of coordinates, the coordination of all the motions of the parts of a molecule is resolved into a series of modes. Each mode has a characteristic relaxation time. The theory produces equations by means of which the relaxation times, the components of the complex viscosity, and the components of the complex rigidity can be calculated from the steady flowviscosities of the solution and the solvent, the molecular weight and concentration of the polymer, and the absolute temperature. Limitations of the theory may arise from the exclusion from consideration of (1) very rapid relaxation processes involving segments shorter than the submolecule and (2) the obstruction of the motion of a segment by other segments with which it happens to be in contact. Another possible cause of disagreement between the theory and experimental data is the polydispersity of any actual polymer; this factor is important because the calculated relaxation times increase rapidly with increasing molecular weight.

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A Theory of the Linear Viscoelastic Properties of Dilute Solutions of Coiling Polymers

We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. The passage of each molecule is detected as a transient decrease of ionic current whose duration is proportional to polymer length. Channel blockades can therefore be used to measure polynucleotide length. With further improvements, the method could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA.

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Characterization of individual polynucleotide molecules using a membrane channel

The problem of the motions of a chain molecule diffusing in a viscous fluid under the influence of external forces or currents is considered for a particular model. This model is a chain of beads connected by ideal springs. Hydrodynamic interaction between the beads is introduced in the approximate form due to Kirkwood and Riseman. It is possible to solve this problem exactly with the use of a transformation to a set of normal coordinates. The viscosity, birefringence of flow, and dielectric and tensile relaxation behavior are calculated explicitly. The intrinsic viscosity in steady flow is somewhat different from the Kirkwood‐Riseman result, and there is no change of viscosity with shear rate. The spectrum of relaxation times is similar to that found by Rouse and by F. Bueche, but has its maximum at a lower frequency than those obtained by Kuhn and Kuhn and by Kirkwood and Fuoss in other ways.

Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss

The transition between the helical and randomly coiled forms of a polypeptide chain is discussed by reference to a simple model that allows bonding only between each group and the third preceding Two principal parameters are introduced, a statistical parameter that is essentially an equilibrium constant for the bonding of segments to a portion of the chain that is already in helical form, and a special correction factor for the initiation of a helix A third parameter which specifies the minimum number of segments in a random section between two helical portions has only a minor effect on the results The partition function for this model is handled in two alternative ways, either as a summation suitable for short chains, or in terms of the eigenvalues and eigenvectors of a characteristic matrix; the latter is more suitable for long chains A transition from the random to the helical form is encountered as either the bonding parameter or the chain length is increased The critical value of the bonding pa

Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains

Formulas for the mean square radii of various branched and ringed polymer molecules are developed under the usual assumptions regarding the statistics of chain configuration. For branched molecules, the mean square radii vary less rapidly with molecular weight than for strictly linear molecules, while for systems containing only rings and unbranched chains the variation is more rapid than for the linear case. These results show that in principle the quantity of branches or of rings can be determined from light‐scattering measurements.

The Dimensions of Chain Molecules Containing Branches and Rings

A radial distribution function of polymer segments in a solution of a high polymer may be defined as a quantity proportional to the density of segments at a given distance from some given segment. An approximate expression is derived for this function for dilute solutions of chain molecules of moderate degrees of polymerization. By Fourier inversion a simple expression for the intensity of light scattering, as a function of angle and concentration, may be obtained.

The Scattering of Light and the Radial Distribution Function of High Polymer Solutions

A photoelectric apparatus for the measurement of the angular dependence of light scattering from solutions is described in detail and its performance is discussed. Methods of calculation for the determination of the average extension of the scattering molecules from the data are described. Data are presented for two fractions of polystyrene in various solvents, showing the effect of changing solvent power and temperature, and also confirming a theoretically derived formula for the concentration dependence of the scattering.

Bruno H. Zimm

Papers

Dynamics of Polymer Molecules in Dilute Solution: Viscoelasticity, Flow Birefringence and Dielectric Loss

Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains

The Dimensions of Chain Molecules Containing Branches and Rings

The Scattering of Light and the Radial Distribution Function of High Polymer Solutions

Apparatus and Methods for Measurement and Interpretation of the Angular Variation of Light Scattering; Preliminary Results on Polystyrene Solutions