Maps of preferential conformation of dipeptides in the structural regions of globular proteins

According to X-ray crystallographic analysis of 46 globular proteins the probability of dipeptides frequency in alpha-helical beta-sheet and random coil conformations has been studied on the basis of which the maps of preferentially conformational state of dipeptide in different elements of secondary structure of proteins have been obtained.     

Analysis of the relationship between side-chain conformation and secondary structure in globular proteins

The relationship between the preferred side-chain dihedral angles and the secondary structure of a residue was examined. The structures of 61 proteins solved to a resolution of 2.0 A (1 A = 0.1 nm) or better were analysed using a relational database to store the information. The strongest feature observed was that the chi 1 distribution for most side-chains in an alpha-helix showed an absence of the g- conformation and a shift towards the t conformation when compared to the non-alpha/beta structures. The exceptions to this tendency were for short polar side-chains that form hydrogen bonds with the main-chain which prefer g+. Shifts in the chi 1 preferences for residues in the beta-sheet were observed. Other side-chain dihedral angles (chi 2, chi 3, chi 4) were found to be influenced by the main-chain. This paper presents more accurate distributions for the side-chain dihedral angles which were obtained from the increased number of proteins determined to high resolution. The means and standard deviations for chi 1 and chi 2 angles are presented for all residues according to the secondary structure of the main-chain. The means and standard deviations are given for the most popular conformations for side-chains in which chi 3 and chi 4 rotations affect the position of C atoms.     

Helix-coil transition theory including long-range electrostatic interactions: application to globular proteins

An extension of the Zimm–Bragg two-state theory for the helix–coil transition in polypeptides, which takes into account the effect of peptide charge–dipole interactions on helix stability, is presented. This new theory incorporates these interactions in an expression that is parameterized on recently obtained experimental data on polypeptides for which electrostatic effects are known to influence helix content. Unlike previous two-state or multistate models, which are parameterized on protein x-ray data, the present theoretical treatment in independent of such protein data. The theoretical model is applied to a series of peptides derived from the C-peptide of ribonuclease A, which have been the object of recent spectroscopic studies. The new theoretical approach can account for most of the structural information derived from studies of these C-peptides, and for overall average helix probabilities that are close in magnitude to those observed for these polypeptides in solution. An application of this new formulation for the prediction of the locations of α-helices in globular proteins from their amino acid sequence is also presented.     

Topology of globular proteins

This paper inquires whether it is reasonable to expect the native structure of proteins to be “knotted”. To this end, some topological properties of polypeptides containing disulfide bridges are discussed using notions from mathematical knot theory and graph theory. The probability of occurrence of knots in random cyclic polymers is calculated as a function of chain length by elementary Monte Carlo methods. The implications of this for protein renaturation and for determining the tertiary structure of proteins are discussed.     

Thermodynamics of globular proteins

The analysis of temperature-induced unfolding of proteins in aqueous solutions was performed. Based on the data of thermodynamic parameters of protein unfolding and using the method of semi-empirical calculations of hydration parameters at reference temperature 298 K, we obtained numerical values of enthalpy, free energy, and entropy which characterize the unfolding of proteins in the ‘gas phase’. It was shown that specific values of the energy of weak intramolecular bonds (?H^int), conformational free energy (?G^conf) and entropy (?S^conf) are the same for proteins with molecular weight 7–25 kDa. Using the energy value (?H^int) and the proposed approach for estimation of the conformational entropy of native protein (S^NC), numerical values of the absolute free energy (G^NC) were obtained.     

Nanofibers made of globular proteins

Strong nanofibers composed entirely of a model globular protein, namely, bovine serum albumin (BSA), were produced by electrospinning directly from a BSA solution without the use of chemical cross-linkers. Control of the spinnability and the mechanical properties of the produced nanofibers was achieved by manipulating the protein conformation, protein aggregation, and intra/intermolecular disulfide bonds exchange. In this manner, a low-viscosity globular protein solution could be modified into a polymer-like spinnable solution and easily spun into fibers whose mechanical properties were as good as those of natural fibers made of fibrous protein. We demonstrate here that newly formed disulfide bonds (intra/intermolecular) have a dominant role in both the formation of the nanofibers and in providing them with superior mechanical properties. Our approach to engineer proteins into biocompatible fibrous structures may be used in a wide range of biomedical applications such as suturing, wound dressing, and wound closure.     

Conformational stability of globular proteins

The conformational stability of ribonuclease T1 has been measured as a function of the variables of most interest to biochemists: temperature, pH, salt concentration, disulfide-bond content and amino acid sequence. The results provide insight into the forces that stabilize globular proteins.     

Thermal stabilities of globular proteins

Statistical thermodynamic theory has recently been developed to account for the stabilities of globular proteins. Here we extend that work to predict the dependence on temperature. Folding is assumed to be driven by solvophobic interactions and opposed by the conformational entropy. The temperature dependence of the solvophobic interaction is taken from the transfer experiments on amino acids by Tanford and Nozaki and on model solutes by Gill and Wads?. One long-standing puzzle has been why proteins denature upon heating, since the solvophobic force to fold strengthens with increasing temperature. This is resolved by the theory, which predicts two first-order phase transitions. "Cold denaturation" is driven principally by the weakening of the solvophobic interaction, but normal denaturation is driven principally by the gain of conformational entropy of the chain. Predictions of the thermodynamic state functions are in reasonable agreement with the calorimetric experiments of Privalov and Khechinashvili. Comparison of the theory with experiments suggests that there may be an additional enthalpic driving force toward folding which is not due to the solvophobic interactions.     

The adsorption of globular proteins

A series of experiments is suggested to elucidate further the nature of the adsorption of globular proteins on polar solid surfaces. Two ratios of surface energies and the total protein volume are used to characterize the expected form of the adsorbed species. A simple model calculation illustrates the approach.     

Foam fractionation of globular proteins

Foam fractionation of bovine serum albumin (BSA) was studied as a model system for potato wastewater. The effects of feed concentration, superficial gas velocity, feed flow rate, bubble size, pH, and ionic strength on the enrichment and recovery of BSA were investigated in a single-stage continuous foam fractionation column. Enrichments ranged from 1.5 to 6.0 and recoveries from 5 to 85%. The feed concentrations were varied from 0.01 to 0.2 wt %, and enrichments were found to increase with lower feed concentrations. Enrichments also increased with lower superficial gas velocities and larger bubble sizes. At sufficiently low feed flow rates, enrichment was found to increase with an increase in the flow rate, eventually becoming insensitive to the feed flow rate at higher values. The pH was varied from 3.5 to 7.0 and ionic strength from 0.001M to 0.2M. The effects of pH and ionic strength were found to be coupled with bubble size. A minimum bubble size was found at pH 4.8, the isoelectric point of BSA, resulting in a minimum in the enrichment. Bubble size, and thus enrichment, was found to increase as the ionic strength decreased from 0.2M to 0.01M. Previous models(1,2) for the hydrodynamics of foam column were extended for a singlestage continuous foam fractionation column for the prediction of enrichment and recovery. The model assumed adsorption equilibrium, infinite surface viscosity, and bubbles of the same size. Though coalescence was formally accounted for in the model by considering bubble size as a function of foam height, calculations for the experimental runs were performed only for the case of no coalescence. Quantitative predictions of enrichment and recovery could not be made with a single representative bubble size because of the broad inlet bubble size distribution as well as broadening of the distribution as a result of coalescence. The experimental enrichments were higher and recoveries were lower than the model predictions, the discrepancy being more pronounced at lower feed concentrations because of increased coalescence. The higher enrichments are due to the predominant effect of internal reflux as a result of coalescence whereas the lower recoveries are a result of detrimental effects of broadening bubble size distributions.     

Salting-in characteristics of globular proteins

Protein solubility, and the formation of various solid phases, is of interest in both bioprocessing and the study of protein condensation diseases. Here we examine the the phase behavior of three proteins (chymosin B, β-lactoglobulin B, and pumpkin seed globulin) previously known to display salting-in behavior, and measure their solubility as a function of pH, ionic strength, and salt type. Although the phase behavior of the three proteins is quantitatively different, general trends emerge. Stable crystal nucleation does not occur within the salting-in region for the proteins examined, despite the crystal being observed as the most stable solid phase. Instead, two types of amorphous phases were found within the salting-in region; additionally, an analog to the instantaneous clouding curve was observed within the salting-in region for chymosin B. Also, protein solutions containing sulfate salts resulted in different crystal morphologies depending on whether Li₂SO₄ or (NH₄)₂SO₄ was used.     

Compressibility-structure relationship of globular proteins

The adiabatic compressibility, -beta s, of 11 globular proteins in water was determined by means of sound velocity measurements at 25 degrees C. All the proteins studied except for subtilisin showed positive -beta s values, indicating the large internal compressibility of the protein molecules. The intrinsic compressibility of proteins free from the hydration effect appeared to be comparable to that of normal ice. The compressibility data for 25 proteins, including 14 reported previously [Gekko, K., & Noguchi, H. (1979) J. Phys. Chem. 83, 2706-2714], were statistically analyzed to examine the correlation of the compressibility with some structural parameters and the amino acid compositions of proteins. It was found that -beta s increases with increasing partial specific volume and hydrophobicity of proteins. The helix element also seemed to be a dynamic domain to increase -beta s. Four amino acid residues (Leu, Glu, Phe, and His) greatly increased -beta s, and another four (Asn, Gly, Ser, and Thr) decreased it. Some empirical equations were derived for the estimation of the -beta s values of unknown proteins on the basis of their amino acid compositions. The volume fluctuations of proteins revealed by the compressibility data were in the range of 30-200 mL/mol, which corresponded to about 0.3% of the total protein volume. The conformational fluctuation seemed to enhance the thermal stability of proteins.     

Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation

A statistical-mechanical model (a noninteracting local structure model) of folding and unfolding transition in globular proteins is described and a formulation is given to calculate the partition function. The process of transition is discussed in this model within the framework of equilibrium statistical mechanics. In order to clarify the range of applicability of such an approach, the characteristics of the folding and unfolding transition in globular proteins are analyzed from the statistical-physical point of view. A theoretical advantage is pointed out in studying folding and unfolding processes taking place as conformational fluctuations in individual protein molecules under macroscopic equilibrium at the melting temperature. In this case, paths of folding and unfolding are shown to be identical in the statistical sense. A key to the noninteracting local structure model lies in the concept of local structures and the assumption of the absence of interactions between local structures. A local structure is defined as a continuous section of the chain which takes the same or similar local conformation as in the native conformation. The assumption of the absence of inter-actions between local structures endows the model with the remarkable character that its partition function can be calculated exactly; thereby the equilibrium population of various conformations along the folding and unfolding paths can be discussed only by a knowledge of the folded native conformation.     

Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins

The noninteracting local-structure model of the folding and unfolding transition in globular proteins, the formulation of which was given in the preceding paper, is applied to the analysis of the two-dimensional lattice model of proteins. The lattice model of proteins is a theoretical tool designed to study the statistical-mechanical aspect of the folding and unfolding transition. Its dynamics have been studied by a method of Monte Carlo simulation. The noninteracting local-structure model reproduces the equilibrium properties of the lattice model obtained previously by computer simulation remarkably well, when the specificity of the long-range interactions is strong. This observation indicates that the basic assumption of the noninteracting local-structure model is equivalent to the assumption of strong specificity of intramolecular interactions. It is argued that by assuming this strong specificity, we can emphasize the correct main paths of folding and unfolding transition. The way local structures grow and/or merge along the most probable path of folding in the lattice model is discussed by the noninteracting local-structure model.