The fluorescence decay of tryptophan residues in native and denatured proteins.

The fluorescence decay kinetics at different ranges of the emission spectrum is reported for 17 proteins. Out of eight proteins containing a single tryptophan residue per molecule, seven proteins display multiexponential decay kinetics, suggesting that variability in protein structure may exist for most proteins. Tryptophan residues whose fluorescence spectrum is red shifted may have lifetimes longer than 7 ns. Such long lifetimes have not been detected in any of the denatured proteins studied, indicating that in native proteins the tryptophans having a red-shifted spectrum are affected by the tertiary structure of the protein. The fluorescence decay kinetics of ten denatured proteins studied obey multiexponential decay functions. It is therefore concluded that the tryptophan residues in denatured proteins can be grouped in two classes. The first characterized by a relatively long lifetime of about 4 ns and the second has a short lifetime of about 1.5 ns. The emission spectrum of the group which is characterized by the longer lifetime is red shifted relative to the emission spectrum of the group characterized by the shorter lifetime. A comparison of the decay data with the quantum yield of the proteins raises the possibility that a subgroup of the tryptophan residues is fully quenched. It is noteworthy that despite this heterogeneity in the environment of tryptophan residues in each denatured protein, almost the same decay kinetics has been obtained for all the denatured proteins studied in spite of the vastly different primary structures. It is therefore concluded that each tryptophan residue interacts in a more-or-less random manner with other groups on the polypeptide chain, and that on the average the different tryptophan residues in denatured proteins have a similar type of environment.     

Conformation of bilirubin oxidase in native and denatured states

The conformation of bilirubin oxidase (EC 1.3.3.5) fromMyrothecium verrucaria was studied by circular dichroism (CD). The far-UV CD spectrum showed a single minimum at 215 nm and a maximum near 198 nm, suggesting the dominance of-sheets. There was another negative band at 187 nm that is absent from the spectra of model-helix or-sheet. CD analysis by the method of Changet al. agreed well with the estimates based on the Chou and Fasman sequence-predictive method, but the Provencher-Glöckner method of CD analysis agreed well with the sequence-predictive method of Garnieret al. AtpH 12 the 215- and 187-nm bands completely disappeared and the protein was denatured. This denaturation was accompanied by the appearance of a large positive band at 250 nm, probably due to ionization of tyrosine residues. In 20 mM sodium dodecyl sulfate the magnitude of the 215-nm band increased, but the spectrum transformed to that of partial helices after heating at 100°C. In 6 M guanidine hydrochloride the far-UV CD spectrum was monotonic and became more negative at the lower wavelength limit (near 212 nm), suggesting that the secondary structure of the protein was disrupted. However, the near-UV CD spectrum retained residual aromatic bands even after heating at 100°C. Thus, our denaturation studies suggest that bilirubin oxidase has a rigid tertiary structure.     

Analysis of heterogeneous fluorescence decays in proteins. Using fluorescence lifetime of 8-anilino-1-naphthalenesulfonate to probe apomyoglobin unfolding at equilibrium

The solvatochromic fluorescent dye 8-anilino-1-naphthalenesulfonate (ANS) is one of the popular probes of protein folding. Folding kinetics is tracked with ANS fluorescence intensity, usually interpreted as a reflection of protein structure-the hydrophobicity of the binding environments. Such simplistic view overlooks the complicated nature of ANS-protein complexes: the fluorescence characteristics are convoluted results of the ground state populational distribution of the probe-protein complex, the structural changes in the protein and the excited state photophysics of the probe. Understanding of the interplay of these aspects is crucial in accurate interpretation of the protein dynamics. In this work, the fluorescence decay of ANS complexed with apomyoglobin at different conformations denatured by pH is modeled. The fluorescence decay of the ANS-apomyoglobin complex contains information on not only apomyoglobin structure but also molecular populational distributions. The challenge in modeling fluorescence decay profiles originates from the convolution of heterogeneous binding and excited-state relaxation of the fluorescent probe. We analyzed frequency-domain fluorescence lifetime data of ANS-apomyoglobin with both maximum entropy methods (MEM) and nonlinear least squares methods (NLLS). MEM recovers a model of two expanding-and-merging lifetime distributions for ANS-apomyoglobin in the equilibrium transition from the native (N) through an intermediate (I-1) to the acid-unfolded state U(A). At pH 6.5 and above, when apomyoglobin is mostly populated at the N-state, ANS-apomyoglobin emits a predominant long-lifetime fluorescence from a relaxed charge transfer state S(1,CT) of ANS, and a short-lifetime fluorescence that is mainly from a nascent excited-state S(1,np) of ANS stabilized by the strong ANS-apomyoglobin interaction. Lowering the pH diminishes the contribution from the S(1,np) state. Meanwhile, more protein molecules become populated at the U(A) state, which exhibits a short lifetime that is not distinguishable from the S(1,np) state. At pH 3.4, when the population of the U(A) becomes significant, the short-lifetime fluorescence comes predominantly from ANS binding to the U(A). Further lowering the pH leads to more exposure of the bound ANS. The long lifetime shifts toward and finally merges with the short lifetime and becomes one broad distribution that stands for ANS binding to the U(A) below pH 2.4. The above expanding-and-merging model is consistent with F-statistic analysis of NLLS models. The consistency of this model with the knowledge from the literature, as well as the continuity of the decay parameters changing upon experimental conditions are also crucial in drawing the conclusions.     

Evolutionary role of posttranslational modifications of proteins,as illustrated by the glycosylation characteristics of the digestive enzyme pancreatic ribonuclease

Summary The glycosylation characteristics of the digestive enzyme ribonuclease are summarized. The evolutionary role of this posttranslational modification is discussed and evidence is presented that selection has much influence on the presence or absence of carbohydrate in glycoproteins and on the positions of the carbohydrate attachment sites.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

巨噬细胞来源、分型及在Ⅰ型糖尿病中的作用

传统观点认为,巨噬细胞对胰岛β细胞的存活和功能不利,从而导致I型糖尿病(type 1 diabetes,T1D)中β细胞功能衰竭,是T1D的主要发病机制之一。然而,最近研究发现,巨噬细胞不仅能在胰腺炎期间保护β细胞,还可在β细胞损伤后调节β细胞增殖和再生。研究显示,巨噬细胞在不同环境中具有向不同功能表型转化的潜力,因此,对T1D的不同作用很可能是其异质性所致。现主要就目前对巨噬细胞的来源和功能的异质性、以及其在胰腺发育和T1D中的作用作一综述。     

Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques

Pulse field gradient NMR methods have been used to determine the effective hydrodynamic radii of a range of native and nonnative protein conformations. From these experimental data, empirical relationships between the measured hydrodynamic radius (R(h)) and the number of residues in the polypeptide chain (N) have been established; for native folded proteins R(h) = 4.75N (0.29)A and for highly denatured states R(h) = 2.21N (0.57)A. Predictions from these equations agree well with experimental data from dynamic light scattering and small-angle X-ray or neutron scattering studies reported in the literature for proteins ranging in size from 58 to 760 amino acid residues. The predicted values of the hydrodynamic radii provide a framework that can be used to analyze the conformational properties of a range of nonnative states of proteins. Several examples are given here to illustrate this approach including data for partially structured molten globule states and for proteins that are unfolded but biologically active under physiological conditions. These reveal evidence for significant coupling between local and global features of the conformational ensembles adopted in such states. In particular, the effective dimensions of the polypeptide chain are found to depend significantly on the level of persistence of regions of secondary structure or features such as hydrophobic clusters within a conformational ensemble.     

Involvement of thiol enzymes in the lysosomal breakdown of native and denatured proteins

We have investigated the effect of thiols on the breakdown of some proteins by extracts from highly purified Triton WR-1339-filled rat liver lysosomes at pH 5 and 38°C.The rate as well as the final degree of hydrolysis of serum albumin, a protein which remains presumably native at pH 5, was stimulated by thiols like dithiothreitol and strongly inhibited by monoiodoacetic acid. These effects were also found with native and performic acid-oxidized ribonuclease, with cytochrome c and with horse radish peroxidase. The digestion of hemoglobin was not stimulated by dithiothreitol, but partly inhibited by monoiodoacetic acid; yeast invertase was not hydrolysed at all.Our results indicate (a) that thiol-cathepsins are essential for the breakdown of many proteins by lysosomes; (b) that apparently native proteins like albumin and ribonuclease can be degraded extensively by lysosomal cathepsins; (c) that this degradation is, to a large extent, an all-or-none reaction.     

Protein dynamics. A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1

Studies using time-resolved fluorescence depolarization were performed on the internal motion of Trp 59 of ribonuclease T1 (EC 3.1.27.3) in the free enzyme, 2'-GMP-enzyme complex and 3'-GMP-enzyme complex. The Trp 59 motion was also studied in the free enzyme using molecular dynamics simulations. Energetic analysis of activation barriers to the Trp 59 motion was performed using both the transition state theory and Kramers' theory. The activation parameters showed a dependence on solvent viscosity indicating the transition state approach in aqueous solution to be inadequate. When taking solvent viscosity contributions into account agreement between the transition state and Kramers' theories was obtained. The results indicate the three enzyme forms to have different conformations with the free enzyme and 3'-GMP-enzyme complex being similar. Comparison of the experimental and theoretical results showed a good agreement on the Trp 59 motion in the free enzyme. Trp 59 appears to vibrate rapidly, with a relaxation time of the order of 1 ps, within free space in the protein matrix and to have a slower motion, with a relaxation time of the order of 100 ps, which is related to breathing of the surrounding protein matrix. Molecular dynamics results indicate high mobility in regions of the enzyme involved in the interaction with the guanine base of the inhibitor or substrate while much lower mobility occurred in residues involved in the catalytic mechanism of ribonuclease T1.     

Hydrogen exchange properties of proteins in native and denatured states monitored by mass spectrometry and NMR.

The extent of deuterium labeling of hen lysozyme, its three-disulfide derivative, and the homologous alpha-lactalbumins, has been measured by both mass spectrometry and NMR. Different conformational states of the proteins were produced by varying the solution conditions. Alternate protein conformers were found to contain different numbers of 2H atoms. Furthermore, measurement in the gas phase of the mass spectrometer or directly in solution by NMR gave consistent results. The unique ability of mass spectrometry to distinguish distributions of 2H atoms in protein molecules is exemplified using samples prepared to contain different populations of 2H-labeled protein. A comparison of the peak widths of bovine alpha-lactalbumin in alternate solution conformations but containing the same average number of 2H atoms showed dramatic differences due to different 2H distributions in the two protein conformers. Measurement of 2H distributions by ESI-MS enabled characterization of conformational averaging and structural heterogeneity. In addition, a time course for hydrogen exchange was examined and the variation in distributions of 2H atom compared with simulations for different hydrogen exchange models. The results clearly show that exchange from the native state of bovine alpha-lactalbumin at 15 degrees C is dominated by local unfolding events.     

Two-dimensional 1H-NMR investigation of ribonuclease T1. Resonance assignments, secondary and low-resolution tertiary structures of ribonuclease T1

Ribonuclease T1 was studied by two-dimensional 1H-NMR spectroscopy. Resonance assignments were obtained for the backbone protons of 95 amino acid residues and most of its side-chain protons using sequence-specific assignment procedures. The secondary structure elements of ribonuclease T1 were identified by an investigation of medium- and long-range nuclear Overhauser effects between the backbone and C beta protons. A low-resolution three-dimensional structure of ribonuclease T1 was deduced from qualitative interpretation of long-range nuclear Overhauser effects.     

Conformational unfolding in the N-terminal region of ribonuclease A detected by nonradiative energy transfer: distribution of interresidue distances in the native, denatured, and reduced-denatured states

Time-dependent fluorescence measurements have been used to determine the distribution of distances between probes attached to residues 1 and (49 + 53) of bovine pancreatic ribonuclease A in the native, denatured, and reduced-denatured states. Measurements were made on donor and on doubly labeled (donor + acceptor) protein in 50% aqueous glycerol solutions at ?30°C and at room temperature. The fluorescence-decay curves were used to compute distribution functions for the interprobe distances. The native protein has a narrow distribution of interprobe distances at ?30°C (high-viscosity medium); this distribution is narrower at room temperature (low-viscosity medium), due primarily to the dynamic flexibility of the probes. Denaturation by 6M guanidine hydrochloride leads to a wider distribution of distances at ?30°C, with a shift of the distribution curve to larger distances, because of the increased disorder of the protein. Reduction of the disulfide bonds by dithiothreitol leads to further decreases in transfer efficiency (a unique distribution curve for the reduced protein was not obtained because of the low transfer efficiency). Both the denatured and reduced-denatured species have average interprobe distances of about 60 Å, compared to 36 Å for the native protein. Reduction of the solvent viscosity leads to nearly monoexponential decay of the donor fluorescence in the doubly labeled derivative. This is interpreted as a manifestation of fast local Brownian motions. It appears that large-scale segmental motions do not take place in the denatured protein within the excited-state lifetime of the donor (ca. 8 ns). The above results indicate that reduced-denatured ribonuclease A has residual structure that limits segmental Brownian motion in the N-terminal segment.     

1H-NMR relaxation studies of native and thermally denatured lysozyme solutions: an isotope dilution experiment

1H-NMR relaxation times are reported for native and thermally denatured lysozyme aqueous solutions measured as the function of the proton mole fraction in the sample. A two-exponential character of proton longitudinal relaxation function was observed for native lysozyme solutions: the fast component was attributed to the non-exchangeable protein protons, the slow one to water protons. Purely exponential decay of longitudinal magnetization was observed for the thermally denatured samples. This has been explained in terms of a fast spin exchange model. The contributions of the protein protons to the water proton relaxation rate in native and thermally denatured samples were determined, too.     

Binding modes of inhibitors to ribonuclease T1 as studied by nuclear magnetic resonance

The binding modes of inhibitors to ribonuclease T1 (RNase T1) were studied by the analyses of 270-MHz proton NMR spectra. The chemical shift changes upon binding of phosphate, guanosine, 2'-GMP, 3'-GMP, 5'-GMP, and guanosine 3',5'-bis(phosphate) were observed as high field shifted methyl proton resonances of RNase T1. One methyl resonance was shifted upon binding of phosphate and guanosine nucleotides but not upon binding of guanosine. Four other methyl resonances were shifted upon binding of guanosine and guanosine nucleotides but not upon binding of phosphate. From the analyses of nuclear Overhauser effects for the pair of H8 and H1' protons, together with the vicinal coupling constants for the pair of H1' and H2' protons, the conformation of the guanosine moiety as bound to RNase T1 is found to be C3'-endo-syn for 2'-GMP and 3'-GMP and C3'-endo-anti for 5'-GMP and guanosine 3',5'-bis(phosphate). These observations suggest that RNase T1 probably has specific binding sites for the guanine base and 3'-phosphate group (P1 site) but not for the 5'-phosphate group (PO site) or the ribose ring. The weak binding of guanosine 3',5'-bis(phosphate) and 5'-GMP to RNase T1 is achieved by taking the anti form about the glycosyl bond. The productive binding to RNase T1 probably requires the syn form of the guanosine moiety of RNA substrates.     

The structure and function of ribonuclease T1. XX. Specific inactivation of ribonuclease T1 by reaction with tosylglycolate.

1. Ribonuclease T1 [EC 3.1.4.8] was inactivated by reaction with tosylglycolate (carboxymethyl rho-toluenesulfonate). At pH 5.5 and 8.0, alkylation of the gamma-carboxyl group of glutamic acid-58 appeared to be the predominant reaction and the major cause of inactivation by tosylglycolate, as in the case of the iodoacetate reaction, although the rate of inactivation was slower than that by iodoacetate. At pH 8.0, histidine residues were also alkylated to some extent. 2. The maximal rate of inactivation was observed at around pH 5.5 and the pH dependence of the rate of inactivation suggested the implication of two groups in the reaction, with apparent pKa values of about 3-4 (possibly histidine residue(s)). 3. In the presence of substrate analogs, ribonuclease T1 was markedly protected from inactivation by tosylglycolate at pH 5.5. The extent of protection corresponded to the binding strength of the substrate analog, except for guanosine. Ribonuclease T1 was much less protected from inactivation by guanosine than by 3'-AMP or 3'-CMP, which has a lower binding strength toward ribonuclease T1. This may indicate that glutamic acid-58 is situated in the catalytic site, at which the phosphate moiety of these nucleotides directly interacts. 4. Enzyme which had been extensively inactivated with tosylglycolate at pH 5.5 scarcely reacted with iodoacetate at pH 5.5, suggesting that these reagents react at the same site, i.e. glutamic acid-58. On the other hand, enzyme which had been inactivated almost completely with tosylglycolate at pH 8.0 still reacted with iodoacetate to some extent at pH 8.0, and the modes of reaction of tosylglycolate and iodoacetate toward ribonuclease T1 appeared to be somewhat different.     

Picosecond time-resolved fluorescence of ribonuclease T1. A pH and substrate analogue binding study.

The tryptophyl fluorescence of ribonuclease T1 decays monoexponentially at pH 5.5, tau = 4.04 ns but on increasing pH, a second short-lived component of 1.5 ns appears with a midpoint between pH 6.5 and 7.0. Both components have the same fluorescence spectrum. Acrylamide quenches both fluorescence components, and the short-lived component is quenched fivefold faster than the predominant long component. Binding of the substrate analogue 2'-guanylic acid at pH 5.5 quenches the fluorescence by 20% and introduces a second decay component, tau = 1.16 ns. Acrylamide quenches both tryptophyl decay components, with similar quenching rates. The fluorescence anisotropy decay of ribonuclease T1 was consistent with a molecule the size of ribonuclease T1 surrounded by a single layer of water at pH 7.4, even though the anisotropy decay at pH 5.5 deviated from Stokes-Einstein behavior. The fluorescence data were interpreted with a model where the tryptophyl residue exists in two conformations, remaining in a hydrophobic pocket. The acrylamide quenching is interpreted with electron transfer theory and suggests that one conformer has the nearest atom approximately 3 A from the protein surface, and the other, approximately 2 A.