ABSTRACT
Kinetics of refolding and unfolding of staphylococcal nuclease and its six mutants, each carrying single or double amino acid substitutions, are studied by stopped-flow circular dichroism measurements. A transient kinetic intermediate formed within 10 ms after refolding starts possesses a substantial part of the N-domain core beta-structure, whereas helices are formed at the later stages. The structure of the kinetic intermediate is less organized than the structure that is known to be formed by a nuclease 1-136 fragment. Only the refolding kinetics are affected by the mutations in all the mutants except two in which the mutations have changed the native structure. From this result and also from the locations of the mutation sites, the major N-terminal domain of the nuclease in the transition state of folding has a structure nearly identical to the native one. On the other hand, the minor C-terminal domain has previously been shown to be still disorganized in the transition state. The effects of the amino acid substitutions on the stability of the native and the transition states are in good agreement with the changes in the hydration free energy, expected for the corresponding amino acid replacements in the unfolded polypeptide. Since side chains of all the mutated residues are not accessible to solvent in the native structure, the result suggests that it is the unfolded state that is mainly affected by the mutations.
Subject(s)
Circular Dichroism , Micrococcal Nuclease/chemistry , Protein Conformation , Staphylococcus aureus/enzymology , Kinetics , Micrococcal Nuclease/genetics , Models, Molecular , Point Mutation , Protein Denaturation , Protein Folding , Recombinant Proteins/chemistry , Staphylococcus aureus/genetics , Urea/pharmacologyABSTRACT
The conformational properties of streptokinase (Sk) have been assessed by several spectroscopic techniques. A solvent accessibility of about 70% of the 22 Tyr residues was found by u.v. perturbation spectroscopy. Fluorescence spectroscopy indicates also the surface localization of the single Trp 6 residue. Circular dichroism (c.d.), infrared (i.r.), and Raman spectra were analysed in order to estimate the contents of secondary structure elements of Sk. Values in the range of 14-23% alpha-helices, 38-46% beta-structures, 10-30% turns and 12-23% residual structures were found. The characteristics of the c.d. spectrum support the classification of Sk as an alpha + beta protein. Effects of temperature, pH, and denaturants were studied by c.d. spectroscopy, and on spin-labelled Sk, by e.p.r. spectroscopy. Structural effects were induced at temperatures above 40 degrees C, pH values below 3.0 and urea concentrations above 2 M. At temperatures above 70 degrees C, at pH 2.1, and at urea and Gu.HCl concentrations of 7 M and 5 M, respectively, no further structural changes are revealed in the spectra. At temperatures around 50 degrees C, at pH 3.0, and denaturant concentrations of about 1 M Gu.HCl and 1 M to 2 M urea, c.d. effects were observed in the near-u.v. region indicating an increase in the asymmetry for aromatic amino acids in comparison with the structure of Sk in low ionic strength buffers at neutral pH, 20 degrees C and in the absence of denaturants. These effects were most pronounced for the temperature dependence of the c.d. spectra. E.p.r. spectroscopy has shown that loosening of the protein surrounding of the spin label already begins at 1 M urea and that the mobility of the spin label points to a structural change in Sk at 46 degrees C.
Subject(s)
Streptokinase/chemistry , Amino Acids/analysis , Circular Dichroism , Electron Spin Resonance Spectroscopy/methods , Hydrogen-Ion Concentration , Protein Conformation , Solvents , Spectrometry, Fluorescence/methods , Spectrophotometry, Ultraviolet/methods , Spectrum Analysis, Raman/methods , Spin Labels , Streptococcus/enzymologyABSTRACT
Infrared spectra of poly(D,L-alanine), poly(L-glutamic acid), poly(L-lysine), silk fibroin, and tropomyosin have been registered for various conformations of the polypeptide chain. Assuming additivity of the main- and side-chain absorption, spectral parameters of amide I and II absorption bands corresponding to alpha-, beta-, and random coil conformations have been derived. The amide I band parameters for H2O and D2O have been compared.
Subject(s)
Amides/chemistry , Protein Conformation , Animals , Circular Dichroism , Fibroins/chemistry , Peptides/chemistry , Polyglutamic Acid/chemistry , Polylysine/chemistry , Rabbits , Spectrophotometry, Infrared , Tropomyosin/chemistry , WaterABSTRACT
Infrared spectra of the amino acid residues in H2O solution have been obtained in the 1800-1400-cm-1 region. It has been established that amino acid residues of arginine, asparagine, glutamine, aspartic and glutamic acids, lysine, tyrosine, histidine, and phenylalanine have intensive absorption in this spectral region. Infrared spectra for a set of model compounds have been measured. On the basis of these data, spectral parameters of amino acid residue absorption bands have been determined.
Subject(s)
Amino Acids/chemistry , Peptides/chemistry , Protein Conformation , Spectrophotometry, Infrared , WaterABSTRACT
Infrared spectra of 13 globular proteins have been obtained in the 1800-1480-cm-1 region for H2O solutions. A method for estimating protein secondary structure from the ir spectrum has been developed. The method can also be used for estimating polypeptide and fibrous protein conformation. For the globular and fibrous proteins and polypeptides analyzed, the correlation coefficients between the ir and x-ray estimates of ordered helix, disordered helix, ordered beta-structure, disordered beta-structure, turns, and remainder were 0.98, 0.80, 0.99, 0.87, 0.90, and 0.92 respectively.
