Thermal behavior of the 760-nm absorption band in photodissociated sperm whale carbonmonoxymyoglobin at cryogenic temperature: dependence on external medium

Mammary Transcriptome Profile during Peak and Late Lactation Reveals Differentially Expression Genes Related to Inflammation and Immunity in Chinese Holstein

Simple Summary

Milk somatic cell count, referring to the total number of somatic cells per milliliter of bovine milk, changes regularly during the lactation cycle. The somatic cell count of healthy cows is usually higher in late lactation than in peak lactation. When the inflammatory response in dairy cow mammary gland becomes more intense, the milk somatic cell count increases together with the reduction of milk quality and yield. Autoimmunity was thought to play an important role in the prevention of mastitis in late lactation of dairy cattle. However, the underlying mechanisms related to the gene expression levels during the process remain unknown. In this study, transcriptome sequencing was performed to screen the differentially expressed genes related to the inflammation and immunity in healthy Chinese Holstein mammary glands. Our findings are helpful to understand the physiological functions of mammary inflammation of Chinese Holstein during late lactation.

Abstract

Somatic cell count (SCC) in milk is widely used in the dairy industry, as an indicator of the health of mammary gland. While the SCC of dairy cattle was higher in late lactation than in peak lactation, its association with gene expressions of mammary gland were largely unknown. In this study, a transcriptomic sequencing approach and bioinformatics analysis were used to investigate the differential expressed genes (DEGs) associated with inflammation and immunity between peak and late periods of lactation in Chinese Holstein. A total of 446 DEGs (padj < 0.05 and fold change >2) were identified, 50 of which belonged to seven pathways and five terms related to inflammation and immunity. Our data suggested that the activation of nuclear transcription factor-κB (NF-κB) pathway and Toll-like receptor signaling pathway caused inflammatory response, and the activation of chemokine signaling pathway and cytokine–cytokine receptor interaction signaling pathway caused a protective immune response to ensure dairy cows health during late lactation. Our findings deepen the understanding of the molecular mechanism and physiological functions of mammary inflammation in Chinese Holstein during late lactation.

Conformational substates of ferricytochrome c revealed by combined optical absorption and electronic circular dichroism spectroscopy at cryogenic temperature

We have investigated the heterogeneity of the Fe(III)-Met80 linkage of horse heart ferricytochrome c by probing the 695nm charge transfer band with absorption and electronic circular dichroism (ECD) spectroscopy. In order to verify the connection between conformational substates of the Fe(III)-Met80 linkage and the 695nm band spectral heterogeneity, we have performed experiments as a function of pH (neutral and acidic) and temperature (room and 20K). At room temperature, the ECD spectrum is blue shifted with respect to the absorption one; the shift is more pronounced at acidic pH and is compatible with the presence of sub-bands. ECD measurements at 20K highlighted the heterogeneous nature of the 695nm band and provided direct experimental evidence for the presence of sub-bands. Indeed, while the absorption spectra remained deceivingly unstructured, the ECD spectra showed well resolved peaks and shoulders. A consistent fit of the 20K absorption and ECD spectra showed that five Gaussians (each centered at the same frequency in the absorption and ECD spectrum) are able to reproduce the observed lineshapes. A careful analysis of frequency shifts and intensity ratios of these sub-bands enabled us to identify at least three distinct sub-bands arising from taxonomic conformational substates of the Fe(III)-Met80 linkage. In view of the major influence of the Fe(III)-Met80 linkage on the redox potential of ferricytochrome c, we speculate that these spectrally distinguishable substates may have different functional roles.

Spectroscopic markers of the T<-->R quaternary transition in human hemoglobin

In this work, we use a sol-gel protocol to trap and compare the R and T quaternary states of both the deoxygenated (deoxyHb) and carbonmonoxide (HbCO) derivatives of human hemoglobin. The near infrared optical absorption band III and the infrared CO stretching band are used to detect the effect of quaternary structure on the spectral properties of deoxyHb and HbCO; comparison with myoglobin allows for an assessment of tertiary and quaternary contributions to the measured band shifts. The R<-->T transition is shown to cause a blue shift of the band III by approximately 35 cm(-1) for deoxyHb and a red shift of the CO stretching band by only approximately 0.3 cm(-1) for HbCO. This clearly shows that quaternary structure changes are transmitted to the heme pocket and that effects on deoxyHb are much larger than on HbCO, at least as far as the band energies are concerned. Experiments performed in the ample temperature interval of 300-10K show that the above quaternary structure effects are "static" and do not influence the dynamic properties of the heme pocket, at least as probed by the temperature dependence of band III and of the CO stretching band. The availability of quaternary structure sensitive spectroscopic markers and the quantitative measurement of the quaternary structure contribution to band shifts will be of considerable help in the analysis of flash-photolysis experiments on hemoglobin. Moreover, it will enable one to characterize the dynamic properties of functionally relevant hemoglobin intermediates and to study the kinetics of both the T-->R and R-->T quaternary transitions through time-resolved spectroscopy.

Internal dynamics and protein–matrix coupling in trehalose-coated proteins

We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water-trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides). Several experimental techniques were used: Mossbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q(B) containing or Q(B) deprived reaction centre from R. sphaeroides. Experimental results, together with the outcome of molecular dynamics simulations, concurred to give a picture of how water-containing matrices control the internal dynamics of the embedded proteins. This occurs, in particular, via the formation of hydrogen bond networks that anchor the protein surface to the surrounding matrix, whose stiffness increases by lowering the sample water content. In the conclusion section, we also briefly speculate on how the protein-matrix interactions observed in our samples may shed light on the protein-solvent coupling also in liquid aqueous solutions.

The effect of ligand dynamics on heme electronic transition band III in myoglobin

Band III is a near-infrared electronic transition at ~13,000 cm(-1) in heme proteins that has been studied extensively as a marker of protein conformational relaxation after photodissociation of the heme-bound ligand. To examine the influence of the heme pocket structure and ligand dynamics on band III, we have studied carbon monoxide recombination in a variety of myoglobin mutants after photolysis at 3 K using Fourier transform infrared temperature-derivative spectroscopy with monitoring in three spectral ranges, (1) band III, the mid-infrared region of (2) the heme-bound CO, and (3) the photodissociated CO. Here we present data on mutant myoglobins V68F and L29W, which both exhibit pronounced ligand movements at low temperature. From spectral and kinetic analyses in the mid-infrared, a small number of photoproduct populations can be distinguished, differing in their distal heme pocket conformations and/or CO locations. We have decomposed band III into its individual photoproduct contributions. Each photoproduct state exhibits a different "kinetic hole-burning" (KHB) effect, a coupling of the activation enthalpy for rebinding to the position of band III. The analysis reveals that the heme pocket structure and the photodissociated CO markedly affect the band III transition. A strong kinetic hole-burning effect results only when the CO ligand resides in the docking site on top of the heme group. Migration of CO away from the heme group leads to an overall blue shift of band III. Consequently, band III can be used as a sensitive tool to study ligand dynamics after photodissociation in heme proteins.

Structural and dynamic properties of the homodimeric hemoglobin from Scapharca inaequivalvis Thr-72-->Ile mutant: molecular dynamics simulation, low temperature visible absorption spectroscopy, and resonance Raman spectroscopy studies

Molecular dynamics simulations, low temperature visible absorption spectroscopy, and resonance Raman spectroscopy have been performed on a mutant of the Scapharca inaequivalvis homodimeric hemoglobin, where residue threonine 72, at the subunit interface, has been substituted by isoleucine. Molecular dynamics simulation indicates that in the Thr-72-->Ile mutant several residues that have been shown to play a role in ligand binding fluctuate around orientations and distances similar to those observed in the x-ray structure of the CO derivative of the native hemoglobin, although the overall structure remains in the T state. Visible absorption spectroscopy data indicate that in the deoxy form the Soret band is less asymmetric in the mutant than in the native protein, suggesting a more planar heme structure; moreover, these data suggest a similar heme-solvent interaction in both the liganded and unliganded states of the mutant protein, at variance with that observed in the native protein. The "conformation sensitive" band III of the deoxy mutant protein is shifted to lower energy by >100 cm-1 with respect to the native one, about one-half of that observed in the low temperature photoproducts of both proteins, indicating a less polar or more hydrophobic heme environment. Resonance Raman spectroscopy data show a slight shift of the iron-proximal histidine stretching mode of the deoxy mutant toward lower frequency with respect to the native protein, which can be interpreted in terms of either a change in packing of the phenyl ring of Phe-97, as also observed from the simulation, or a loss of water in the heme pocket. In line with this latter interpretation, the number of water molecules that dynamically enters the intersubunit interface, as calculated by the molecular dynamics simulation, is lower in the mutant than in the native protein. The 10-ns photoproduct for the carbonmonoxy mutant derivative has a higher iron-proximal histidine stretching frequency than does the native protein. This suggests a subnanosecond relaxation that is slowed in the mutant, consistent with a stabilization of the R structure. Taken together, the molecular dynamics and the spectroscopic data indicate that the higher oxygen affinity displayed by the Thr-72-->Ile mutant is mainly due to a local perturbation in the dimer interface that propagates to the heme region, perturbing the polarity of the heme environment and propionate interactions. These changes are consistent with a destabilization of the T state and a stabilization of the R state in the mutant relative to the native protein.

Spectroscopic effects of polarity and hydration in the distal heme pocket of deoxymyoglobin

Distal pocket mutations at the E7 position (His64) of sperm whale deoxymyoglobin (deoxyMb) are used as a probe of distal pocket polarity and hydration. Changes of two key spectroscopic markers, the Fe-His(F8) stretch in the resonance Raman spectrum and the position of band III in the absorption spectrum, are monitored as the His64Tyr, His64Phe, His64Leu, and His64Gly mutations alter the distal heme pocket environment. The Fe-His vibration for the Phe, Leu, and Gly mutants is shifted to a lower frequency by 1-2 cm-1 relative to the Tyr mutant, wild type (WT), and native deoxyMb. Band III shifts to the red by approximately 4 nm ( approximately 70 cm-1) relative to WT and native deoxyMb for all the His64 mutants examined in this work. We correlate the small shift in the Fe-His frequency to the local electrostatic environment directly above the heme iron, affected by the presence of a localized water molecule in the heme pocket that is hydrogen-bonded to the E7 residue. The position of band III is roughly correlated to the displacement of the iron from the heme plane; however, the relatively large scatter in this correlation, as well as its dependence on distal pocket mutations, suggests that the heme pocket environment, particularly the E7 residue, also affects the energy of this transition.

Near infrared absorption spectra of human deoxy- and oxyhaemoglobin in the temperature range 20-40 degrees C

Temperature-dependent spectral changes of human haemoglobin A (HbA) derivatives were investigated in the range 20-40 degrees C. The intensity of the deoxy-HbA decreased by 3-3.5%, while that of oxy- and met-HbA by less than 1%, when the temperature increased from 20 degrees to 40 degrees C. The present findings can be employed to improve the algorithms used in in vivo near infrared spectroscopy.

Heme geometry in the 10 K photoproduct from sperm whale carbonmonoxymyoglobin

We have measured the Soret band of the photoproduct obtained by complete photolysis of sperm whale carbonmonoxymyoglobin at 10 K. The experimental spectrum has been modeled with an analytical expression that takes into account the homogeneous bandwidth, the coupling of the electronic transition with both high and low frequency vibrational modes, and the effects of static conformational heterogeneity. The comparison with deoxymyoglobin at low temperature reveals three main differences. In the photoproduct, the Soret band is shifted to red. The band is less asymmetric, and an enhanced coupling to the heme vibrational mode at 674 cm-1 is observed. These differences reflect incomplete relaxation of the active site after ligand dissociation. The smaller band asymmetry of the photoproduct can be explained by a smaller displacement of the iron atom from the mean porphyrin plane, in quantitative agreement with the X-ray structure analysis. The enhanced vibrational coupling is attributed to a subtle heme distortion from the planar geometry that is barely detectable in the X-ray structure.

Near-infrared spectra of Scapharca homodimeric hemoglobin: characterization of the deoxy and photodissociated derivatives

The near-infrared charge transfer band at 760 nm (band III) has been investigated in deoxy and photodissociated dimeric Scapharca hemoglobin. At 300 K, the 10-ns spectrum of the carbonmonoxy derivative photoproduct is shifted by about 6 nm toward longer wavelengths with respect to the deoxy spectrum, both in buffer and in glycerol/buffer solutions. Moreover, the band III peak occurs at about the same wavelength at 300 K and at 10 K for the 10-ns photodissociated derivative, whereas in the deoxy derivative large changes in peak position and linewidth are observed as a function of temperature. These findings suggest that in dimeric Scapharca hemoglobin the photoproduct has not relaxed after 10 ns. The complete time dependence of the relaxation process has been studied both in buffer and in glycerol/buffer solutions at room temperature. The relaxation from the photoproduct to the deoxy species occurs on a microsecond time scale, in line with recent optical absorption and resonance Raman measurements.

Structural heterogeneity of the Fe(2+)-N epsilon (HisF8) bond in various hemoglobin and myoglobin derivatives probed by the Raman-active iron histidine stretching mode

We have examined the Fe(2+)-N epsilon (HisF8) complex in hemoglobin A (HbA) by measuring the band profile of its Raman-active nu Fe-His stretching mode at pH 6.4, 7.0, and 8.0 using the 441-nm line of a HeCd laser. A line shape analysis revealed that the band can be decomposed into five different sublines at omega 1 = 195 cm-1, omega 2 = 203 cm-1, omega 3 = 212 cm-1, omega 4 = 218 cm-1, and omega 5 = 226 cm-1. To identify these to the contributions from the different subunits we have reanalyzed the nu Fe-His band of the HbA hybrids alpha(Fe)2 beta(Co)2 and alpha(Co)2 beta(Fe)2 reported earlier by Rousseau and Friedman (D. Rousseau and J. M. Friedman. 1988. In Biological Application on Raman Spectroscopy. T. G. Spiro, editor, 133-216). Moreover we have reanalyzed other Raman bands from the literature, namely the nu Fe-His band of the isolated hemoglobin subunits alpha SH- and beta SH-HbA, various hemoglobin mutants (i.e., Hb(TyrC7 alpha-->Phe), Hb(TyrC7 alpha-->His), Hb M-Boston and Hb M-Iwate), N-ethylmaleimide-des(Arg141 alpha) hemoglobin (NES-des(Arg141 alpha)HbA) and photolyzed carbonmonoxide hemoglobin (Hb*CO) measured 25 ps and 10 ns after photolysis. These molecules are known to exist in different quaternary states. All bands can be decomposed into a set of sublines exhibiting frequencies which are nearly identical to those found for deoxyhemoglobin A. Additional sublines were found to contribute to the nu Fe-His band of NES-des(Arg141 alpha) HbA and the Hb*CO species. The peak frequencies of the bands are determined by the most intensive sublines. Moreover we have measured the nu Fe-His band of deoxyHbA at 10 K in an aqueous solution and in a 80% glycerol/water mixture. Its subline composition at this temperature depends on the solvent and parallels that of more R-like hemoglobin derivatives. We have also measured the optical charge transfer band III of deoxyHbA at room temperature and found, that at least three subbands are required to fit its asymmetric band shape. This corroborates the findings on the nu Fe-His band in that it is indicative of a heterogeneity of the Fe(2+)-N epsilon(HisF8) bond. Finally we measured the nu Fe-His band of horse heart deoxyMb at different temperatures and decomposed it into three different sublines. In accordance with what was obtained for HbA their intensities rather than their frequencies are temperature-dependent. By comparison with VFe-His bands of some Mb mutants (i.e., Mb(His E7.->Gly) and Mb(HisE7__*Met) we suggest that these sublines may be attributed to different conformations of the heme pocket. Our data show, that the V Fe-His band is governed by at least two different coordinates x and y determining its frequency and intensity, respectively. While the former can be assigned to the tilt angle theta between the Fe2+-NJ(HisF8) bond and the heme normal and/or to the displacement delta of the iron from the heme plane, variations in the intensity may be caused by changes of the azimuthal angle phi formed by the projection of the proximal imidazole and the N(l)-Fe2+-N(III) line of the heme. The sublines are therefore interpreted as resulting from different conformational substates of the Fe2+-N(HisFa) complex which differ in terms of x (theta and/or delta). Each of them may further be subdivided in sub-substates with respect to the coordinate y (theta). Quaternary and tertiary transitions of the protein alter the population of these substates thus giving rise to a redistribution of the VFe-HiS sublines which shifts the corresponding peak frequency to higher values.

Nonexponential protein relaxation: dynamics of conformational change in myoglobin

The picosecond evolution of the tertiary conformation of myoglobin (Mb) after photodissociation of MbCO was investigated at room temperature by probing band III, a weak iron-porphyrin charge-transfer transition near 13,110 cm-1 (763 nm) that is sensitive to the out-of-plane displacement of the iron. Upon photolysis, the iron moves out of the plane of the porphyrin, causing a blue-shift of band III and a concomitant change in the protein conformation. The dynamics for this functionally important motion are highly nonexponential, in agreement with recent molecular dynamics simulations [Kuczera, K., Lambry, J.-C., Martin, J.-L. & Karplus, M. (1993) Proc. Natl. Acad. Sci. USA 90, 5805-5807]. The conformational change likely affects the height of the barrier to ligand rebinding and may explain nonexponential NO rebinding.

Spectroscopic evidence for conformational relaxation in myoglobin

The time and temperature dependencies of the line area (M0) and position (M1) of band III at approximately 760 nm have been measured with Fourier-transform infrared spectroscopy in deoxymyoglobin (Mb) and continuously photolyzed carbon monoxide myoglobin (MbCO). Below 200 K, the area of band III in the photoproduct Mb* increases with time even on time scales of hours. This behavior indicates changes in the distribution of activation enthalpy barriers for ligand rebinding under extended illumination. The band position of Mb* shifts to higher wavenumbers with increasing temperature up to 100 K owing to kinetic hole burning; the same protein coordinate that controls the position of band III also determines the rebinding barrier height. The shift ceases above 100 K, implying that more than one protein coordinate affects the height of the rebinding barrier. Above 160 K, the line position in Mb* shifts again and coalesces with the value of Mb for temperatures above 200 K. The shift is accompanied by an increase of the line area, reflecting a slowing of rebinding kinetics. Both effects are explained in the framework of the model introduced by Steinbach et al. [(1991) Biochemistry 30, 3988-4001]. Above approximately 160 K, the conformational relaxation Mb*----Mb simultaneously shifts the line position of band III and increases the enthalpy barrier for ligand rebinding. Furthermore, equilibrium fluctuations lead to an averaging of the band position and the rebinding enthalpy.

Protein dynamics. Comparative investigation on heme-proteins with different physiological roles

We report the low temperature carbon monoxide recombination kinetics after photolysis and the temperature dependence of the visible absorption spectra of the isolated alpha SH-CO and beta SH-CO subunits from human hemoglobin A in ethylene glycol/water and in glycerol/water mixtures. Kinetic measurements on sperm whale (Physeter catodon) myoglobin and previously published optical spectroscopy data on the latter protein and on human hemoglobin A, in both solvents, (Cordone, L., A. Cupane, M. Leone, E. Vitrano, and D. Bulone. 1988. J. Mol. Biol. 199:312-218) are taken as reference. Low temperature flash photolysis data are analyzed within the multiple substates model proposed by Frauenfelder and co-workers (Austin, R. H., K. W. Beeson, L. Eisenstein, H. Frauenfelder, and I. C. Gunsalus. 1975. Biochemistry. 14:5355-5373). Within this model a distribution of activation enthalpies for ligand binding accounts for the structural heterogeneity of the protein, while the preexponential factor, containing also the entropic contribution to the free energy of the process, is considered to be constant for all conformational substates. Optical spectra are deconvoluted in gaussian components and the temperature dependence of the moments of the resulting bands is analyzed, within the harmonic Frank-Condon approximation, to obtain information on the stereodynamic properties of the heme pocket. The kinetic and spectral parameters thus obtained are found to be protein dependent also with respect to their sensitivity to changes in the composition of the external medium. A close correlation between the kinetic and spectral features is observed for the proteins examined under all experimental conditions studied. The results reported are discussed in terms of differences in the heme pocket structure and in the conformational heterogeneity among the various proteins, as related to their different capability to accommodate constraints imposed by the external medium.