Large-scale oscillatory motions in myoglobin

Elastic and inelastic components of neutron scattering from lyophilized myoglobin were measured at wavevector transfers, Q of 1.0, 1.4, 1.85, and 3.0 Å^-1 and at temperatures of 77 and 298 K. The elastic scattering determines an overall effective mean square atomic displacement which was employed in a simple harmonic Langevin formalism to obtain effective force constants describing molecular deformations. These force constants and the inelastic data are compatible with alpha helices as a vibrating species at room temperature, and with amino acid residues as the vibrating entities at 77 K. The present measurements are consistent with recent molecular dynamics calculations.     

Internal protein motions, concentrated glycerol, and hydrogen exchange studied in myoglobin

Experiments were carried out to measure the effect of concentrations of glycerol on H-exchange (HX) rates by using myoglobin as a test protein. Concentrated glycerol has only a small slowing effect on the HX kinetics of freely exposed amides, studied in a small molecule model (acetamide). Larger effects occur in structured proteins. The effect of solvent glycerol on different parts of the HX curve of myoglobin was studied by use of a selective "kinetic labeling" approach. Concentrated glycerol exerts an apparently reverse effect on protein H exchange; the faster exchanging "surface" protons are least affected, while the slower and slower amide NH is further slowed by larger and larger factors. These results seem inconsistent with solvent penetration models which generally visualize slower and slower protons as being placed, and undergoing exchange, farther and farther from the solvent-protein interface. On the other hand, the results are as expected for the local unfolding model for protein H exchange since concentrated glycerol is known to stabilize proteins against unfolding. In the local unfolding model, slower exchanging protons are released by way of higher energy and therefore generally larger, unfolding reactions. Larger unfoldings must be more inhibited by the glycerol effect.     

Folding myoglobin within a sol-gel glass: protein folding constrained to a small volume

The unfolding and refolding reaction of myoglobin was examined in solution and within a porous silica sol-gel glass. The sol-gel pores constrain the protein to a volume that is the same size and shape as the folded native state accompanied by a few layers of water solvation. Denaturants such as low pH buffers can be diffused through the gel pores to the protein to initiate unfolding and refolding. Acid-induced unfolding was hindered by the steric constraints imposed by the gel pores such that more denaturing conditions were required within the gel than in solution to create the unfolded state. No new folding intermediates were observed. Refolding of myoglobin was not complete in millimolar pH 7 buffer alone. Addition of 25% glycerol to the pH 7 buffer resulted in nearly complete refolding, and the use of 1 M phosphate buffer resulted in complete refolding. The role of this cosolvent and salt in disrupting the ordered water surrounding the protein within the gel is discussed in light of the Hofmeister series and entropic trapping via a diminished hydrophobic effect within the gel. These results are consistent with the premises of folding models in which secondary and tertiary structures are considered to form within a compact conformation of the protein backbone.     

Properties of monoclonal antibodies specific for determinants of a protein antigen, myoglobin

Monoclonal hybridoma antibodies specific for the protein antigen sperm whale myoglobin were produced using hyperimmune spleen cells from mice with the genetic trait of high responsiveness to myoglobin. Antibodies from the several clones tested were found to produce linear Scatchard plots, as predicted for homogeneous antibodies, and to possess high affinities for the immunogen (KA congruent to 10(9) M-1). None of the monoclonal antibodies tested reacted with either fragment (1-55) or fragment (132-153) of sperm whale myoglobin. Competitive binding assays using human and horse myoglobins suggested that several of these monoclonal antibodies, which can readily distinguish these myoglobins, recognize different antigenic determinants on the myoglobin molecule. Studies using additional myoglobin sequence variants as competitors should be able to more closely define these antigenic determinants.     

Proximal ligand motions in H93G myoglobin.

Resonance Raman spectroscopy has been used to observe changes in the iron-ligand stretching frequency in photoproduct spectra of the proximal cavity mutant of myoglobin H93G. The measurements compare the deoxy ferrous state of the heme iron in H93G(L), where L is an exogenous imidazole ligand bound in the proximal cavity, to the photolyzed intermediate of H93G(L)*CO at 8 ns. There are significant differences in the frequencies of the iron-ligand axial out-of-plane mode nu(Fe-L) in the photoproduct spectra depending on the nature of L for a series of methyl-substituted imidazoles. Further comparison was made with the proximal cavity mutant of myoglobin in the absence of exogenous ligand (H93G) and the photoproduct of the carbonmonoxy adduct of H93G (H93G-*CO). For this case, it has been shown that H2O is the axial (fifth) ligand to the heme iron in the deoxy form of H93G. The photoproduct of H93G-*CO is consistent with a transiently bound ligand proposed to be a histidine. The data presented here further substantiate the conclusion that a conformationally driven ligand switch exists in photolyzed H93G-*CO. The results suggest that ligand conformational changes in response to dynamic motions of the globin on the nanosecond and longer time scales are a general feature of the H93G proximal cavity mutant.     

Molecular dynamics simulations of heme reorientational motions in myoglobin.

Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes in the protein.     

Radially softening diffusive motions in a globular protein

Molecular dynamics simulation, quasielastic neutron scattering and analytical theory are combined to characterize diffusive motions in a hydrated protein, C-phycocyanin. The simulation-derived scattering function is in approximate agreement with experiment and is decomposed to determine the essential contributions. It is found that the geometry of the atomic motions can be modeled as diffusion in spheres with a distribution of radii. The time dependence of the dynamics follows stretched exponential behavior, reflecting a distribution of relaxation times. The average side chain and backbone dynamics are quantified and compared. The dynamical parameters are shown to present a smooth variation with distance from the core of the protein. Moving outward from the center of the protein there is a progressive increase of the mean sphere size, accompanied by a narrowing and shifting to shorter times of the relaxation time distribution. This smooth, "radially softening" dynamics may have important consequences for protein function. It also raises the possibility that the dynamical or "glass" transition with temperature observed experimentally in proteins might be depth dependent, involving, as the temperature decreases, progressive freezing out of the anharmonic dynamics with increasing distance from the center of the protein.     

A temperature-sensitive mutant of Sacchromyces cerevisiae defective in the specific phosphatase of trehalose biosynthesis

Abstract A temperature-sensitive mutant of Saccharomyces cerevisiae has been isolated which accumulates a large pool of trehalose-6-phosphate when shifted to temperatures above 34°C nonpermissive for growth. This indicates that its defect is in the second enzyme of trehalose biosynthesis, the hydrolase that converts trehalose-6-phosphate to trehalose. Trehalose is made continouosly when yeast is growing on high glucose or when it is starved for a nitrogen source, and accumulates as cells enter the stationary phase. Revertants of the mutant able to grow at 37°C arise spontaneously and no longer accumulate trehalose-6-phosphate at this temperature. Also the kinetics of trehalose-6-phosphate accumulation in the mutant following a 25–37°C shift resemble the kinetics of inhibition of RNA and protein synthesis. It is probable therefore that accumulation of high levels of this metabolic intermediate is inhibitory to growth.     

Effect of trehalose on protein structure

Trehalose is a ubiquitous molecule that occurs in lower and higher life forms but not in mammals. Till about 40 years ago, trehalose was visualized as a storage molecule, aiding the release of glucose for carrying out cellular functions. This perception has now changed dramatically. The role of trehalose has expanded, and this molecule has now been implicated in a variety of situations. Trehalose is synthesized as a stress‐responsive factor when cells are exposed to environmental stresses like heat, cold, oxidation, desiccation, and so forth. When unicellular organisms are exposed to stress, they adapt by synthesizing huge amounts of trehalose, which helps them in retaining cellular integrity. This is thought to occur by prevention of denaturation of proteins by trehalose, which would otherwise degrade under stress. This explanation may be rational, since recently, trehalose has been shown to slow down the rate of polyglutamine‐mediated protein aggregation and the resultant pathogenesis by stabilizing an aggregation‐prone model protein. In recent years, trehalose has also proved useful in the cryopreservation of sperm and stem cells and in the development of a highly reliable organ preservation solution. This review aims to highlight the changing perception of the role of trehalose over the last 10 years and to propose common mechanisms that may be involved in all the myriad ways in which trehalose stabilizes protein structures. These will take into account the structure of trehalose molecule and its interactions with its environment, and the explanations will focus on the role of trehalose in preventing protein denaturation.     

The glass transition temperature of mixtures of trehalose and hydroxyethyl starch

Although mixtures of HES and sugars are used to preserve cells during freezing or drying, little is known about the glass transition of HES, or how mixtures of HES and sugars vitrify. These difficulties may be due to the polydispersity between HES samples or differences in preparation techniques, as well as problems in measuring the glass transition temperature (T(g)) using differential scanning calorimetry (DSC). In this report, we examine the T(g) of mixtures of HES and trehalose sugar with <1% moisture content using DSC measurements. By extrapolating these measurements to pure HES using the Gordon-Taylor and Fox equations, we were able to estimate the T(g) of our HES sample at 44 degrees C. These results were additionally confirmed by using mixtures of glucose-HES which yielded a similar extrapolated T(g) value. Our approach to estimating the glass transition temperature of HES may be useful in other cases where glass transitions are not easily identified.     

Conformational substates and motions in myoglobin. External influences on structure and dynamics.

Myoglobin, a simppe dioxygen-storage protein, is a good laboratory for the investigation of the connection between protein structure, dynamics, and function. Fourier-transform infrared spectroscopy on carbon-monoxymyoglobin (MbCO) shows three major CO bands. These bands are excellent probes for the investigation of the structure-function relationship. They have different CO binding kinetics and their CO dipoles form different angles with respect to the heme normal, implying that MbCO exists in three major conformational substates, A0, A1, and A3. The entropies and enthalpies of these substates depend on temperature above approximately 180 K and are influenced by pH, solvent, and pressure. These results suggest that even a protein as simple as Mb can assume a small number of clearly different structures that perform the same function, but with different rates. Moreover, protein structure and dynamics depend strongly on the interaction of the protein with its environment.     

Introduction of a specific binding domain on myoglobin surface by new chemical modification

A new myoglobin, reconstituted with a modified zinc protoporphyrin, having a total of four ammonium groups at the terminal of the two propionate side chains was constructed to introduce a substrate binding site. The protein with a positively charged patch on the surface formed a stable complex with negatively charged substrates, such as hexacyanoferrate(III) and anthraquinonesulfonate via an electrostatic interaction. The complexation was monitored by fluorescence quenching due to singlet electron transfer from the photoexcited reconstituted zinc myoglobin to the substrates. The binding properties were evaluated by Stern-Volmer plots from the fluorescence quenching of the zinc myoglobin by a quencher. Particularly, anthraquinone-2,7-disulfonic acid showed a high affinity with a binding constant of 1.5 x 10(5) M(-1) in 10 mM phosphate buffer, pH 7.0. In contrast, the plots upon the addition of anthraquinone-2-sulfonic acid at different ionic strengths indicated that the complex was formed not only by an electrostatic interaction but also by a hydrophobic contact. The findings from the fluorescence studies conclude that the present system is a useful model for discussion of electron transfer via non-covalently linked donor-acceptor pairing on the protein surface.     

Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants

Ligand migration and binding are central to the biological functions of many proteins such as myoglobin (Mb) and it is widely thought that protein breathing motions open up ligand channels dynamically. However, how a protein exerts its control over the opening and closing of these channels through its intrinsic dynamics is not fully understood. Specifically, a quantitative delineation of the breathing motions that are needed to open ligand channels is lacking. In this work, we present and apply a novel normal mode‐based method to quantitatively delineate what and how breathing motions open ligand migration channels in Mb and its mutants. The motivation behind this work springs from the observation that normal mode motions are closely linked to the breathing motions that are thought to open ligand migration channels. In addition, the method provides a direct and detailed depiction of the motions of each and every residue that lines a channel and can identify key residues that play a dominating role in regulating the channel. The all‐atom model and the full force‐field employed in the method provide a realistic energetics on the work cost required to open a channel, and as a result, the method can be used to efficiently study the effects of mutations on ligand migration channels and on ligand entry rates. Our results on Mb and its mutants are in excellent agreement with MD simulation results and experimentally determined ligand entry rates. Proteins 2015; 83:757–770. © 2015 Wiley Periodicals, Inc.     

The reduction of ferryl myoglobin by ergothioneine: a novel function for ergothioneine

In this paper, we demonstrate that ergothioneine (ES), a naturally occurring thiolhistidine, reduces ferrylmyoglobin (MbIV) to MbIII when the former (ferryl species) is produced by exposing either deoxy MbII or MbIII to H2O2. The reduction of MbIV to MbIII by ES yields the disulfide of ES which the addition of GSH promptly reduces back to ES. The addition of ES (100 microM) in the perfusion buffer of Langendorff rat heart preparations exposed to a brief period of ischemia prevents the myocardial damage (lactate dehydrogenase release) which accompanies reperfusion. The results of these experiments support a view that ES and its redox couple GSH might function in a Mb redox cycle.     

Kinetics of reversible protein denaturation. A study on aplysia myoglobin

The kinetics of denaturation and renaturation of Aplysia Myoglobin by temperature-jump and stopped-flow are reported. The time course of the unfolding and refolding reveals the presence of significant amounts of intermediates both in absence and in the presence of alcohols. A linear three states reaction mechanism is proposed and discussed.     

Translational and rotational motions of proteins in a protein crowded environment

Fluorescence correlation spectroscopy (FCS) was used to measure the translational diffusion of labeled apomyoglobin (tracer) in concentrated solutions of ribonuclease A and human serum albumin (crowders), as a quantitative model system of protein diffusive motions in crowded physiological environments. The ratio of the diffusion coefficient of the tracer protein in the protein crowded solutions and its diffusion coefficient in aqueous solution has been interpreted in terms of local apparent viscosities, a molecular parameter characteristic for each tracer-crowder system. In all protein solutions studied in this work, local translational viscosity values were larger than the solution bulk viscosity, and larger than rotational viscosities estimated for apomyoglobin in the same crowding solutions. Here we propose a method to estimate local apparent viscosities for the tracer translational and rotational diffusion directly from the bulk viscosity of the concentrated protein solutions. As a result of this study, the identification of protein species and the study of hydrodynamic changes and interactions in model crowded protein solutions by means of FCS and time-resolved fluorescence depolarization techniques may be expected to be greatly simplified.     

Partial purification and properties of a highly specific trehalose phosphate phosphatase from Mycobacterium smegmatis

A specific trehalose phosphate phosphatase was purified approximately 50-fold from Mycobacterium smegmatis. The enzyme had a pH optimum of about 7.0 and was stimulated by Mg(2+). The optimum concentration of Mg(2+) was about 1.5 x 10(-3)m. Of other divalent cations tested, only Co(2+) showed some activity. The K(m) for trehalose phosphate was found to be about 1.5 x 10(-3)m. The enzyme showed slight activity toward mannose-6-P and fructose-6-P but was inactive on a large number of other phosphorylated compounds. Citrate was a competitive inhibitor of the enzyme both with respect to trehalose phosphate concentration and Mg(2+) concentration. This inhibition appears to be due to chelation of Mg(2+) by this compound. Ethylenediaminetetraacetic acid and NaF were also inhibitors of the enzyme, but these inhibitions were noncompetitive.     

Comparative protein interactomics of neuroglobin and myoglobin

Neuroglobin is a hypoxia-inducible O(2) -binding protein with neuroprotective effects in cell and animal models of stroke and Alzheimer's disease. The mechanism underlying neuroglobin's cytoprotective action is unknown, although several possibilities have been proposed, including anti-oxidative and anti-apoptotic effects. We used affinity purification-mass spectrometry methods to identify neuroglobin-interacting proteins in normoxic and hypoxic murine neuronal (HN33) cell lysates, and to compare these interactions with those of a structurally and functionally related protein, myoglobin. We report that the protein interactomes of neuroglobin and myoglobin overlap substantially and are modified by hypoxia. In addition, neuroglobin-interacting proteins include partners consistent with both anti-oxidative and anti-apoptotic functions, as well as with a relationship to several neurodegenerative diseases.     

A specific DIF binding protein in Dictyostelium

Differentiation Inducing Factor (DIF-1), a small chlorinated organic molecule which is produced during Dictyostelium development, is believed to be the morphogen that controls the stalk-specific pathway of differentiation. We describe the identification and characterization of a protease-sensitive activity from cell lysates which binds tritiated DIF-1 with the properties expected of a DIF receptor. Scatchard and linear subtraction plots show a single class of binding sites, of high affinity (Kd = 1.8 nM) and low abundance (1100 sites/cell). The activity elutes from heparin-agarose as a single peak. Various DIF-1 analogues compete for binding in proportion to their activities in a stalk cell differentiation bioassay. The amount of binding activity is developmentally regulated, peaking shortly before the appearance of the prestalk-prespore pattern and before the developmental rise in DIF concentration; the rise occurs at the same time that prestalk-specific genes become DIF inducible. Addition of cyclic AMP to aggregated cells, which induces post-aggregative gene expression in general, also induces the binding activity.