Structural and functional roles of modules in hemoglobin. Substitution of module M4 in hemoglobin subunits

Spectroscopic characterization, calorimetric study and molecular docking to evaluate the bioconjugation of maltol with hemoglobin

Maltol, a food additive, is extensively used in our daily life. To date, its biological safety is still debated. In this article, binding interaction of maltol with bovine hemoglobin (BHb), an important functional protein, was studied by molecular docking research and spectroscopic and calorimetric measurements. We found that maltol could cause structural changes of BHb. By interacting with Glu 101 (1.27 Å) and Lys 104 (2.49 Å) residues, maltol changed the cavity structure and induced a microenvironment change around tryptophan (Trp) residue. Thermodynamic parameters obtained from isothermal titration calorimetry (ITC) measurement showed that hydrophobic forces were the main forces existing in this system. The association constant of K (8.0 ± 3.4 × 10⁴  M^-1 ) shows the mild ligand-protein binding for maltol with BHb. The α-helix amount in BHb increased (59.6-62.6%) with different concentrations of maltol and the intrinsic fluorescence intensity was quenched by maltol, indicating the conformation changes and denaturation of BHb. This work presents the interactions of maltol with BHb at the molecular level and obtains evidence that maltol induces adverse effects to proteins in vitro.

Spectroscopic investigation of the effects of aqueous-phase prepared CdTe quantum dots on protein hemoglobin at the molecular level

3-Mercaptopropionic Acid-modified CdTe quantum dots (QDs) were synthesized and characterized by infrared, fluorescence, and ultraviolet-visible absorption spectra and Nano-ZetaSizer measurements. Then the interaction between QDs and hemoglobin was studied to investigate the effects of QDs on the structure and function of hemoglobin by using a variety of spectroscopy methods and isothermal titration calorimetry. The results showed van der Waals forces and hydrogen bonding predominantly played major roles in the binding. The intrinsic fluorescence of hemoglobin was quenched with changes to the microenvironment of tyrosine and tryptophan residues and complex conformational changes of hemoglobin were induced with the loosening and unfolding skeleton. However, the heme in hemoglobin was still stable, indicating that the main physiological function of hemoglobin might not be significantly inhibited. This study will provide a new strategy to study the biological toxicity of QDs at the molecular level.

Preparation and characterization of a chimeric zebrafish-human neuroglobin engineered by module substitution

Neuroglobin (Ngb) is a recently discovered vertebrate heme protein that can reversibly bind oxygen that is expressed in the brain. Zebrafish and human Ngb share about 50% amino acid sequence identity. These Ngb proteins consist of four compact protein structural unit "modules" referred to as M1-M4. In the present study, we investigated the effects of module substitution on the properties of Ngb. Specifically, we prepared and characterized a chimeric ZHZZ Ngb in which the heme-binding module M2 of zebrafish Ngb was replaced by the comparable human Ngb module. Our results showed that the chimeric ZHZZ was stable and formed almost the identical heme-environmental and alpha-helical structure as the human and zebrafish Ngb proteins, suggesting that the structure of Ngb has been evolutionarily conserved.

Identification of residues in human neuroglobin crucial for Guanine nucleotide dissociation inhibitor activity

Neuroglobin (Ngb) is a recently discovered vertebrate heme protein that is expressed in the brain and can reversibly bind oxygen. We previously demonstrated that ferric human Ngb binds to the alpha-subunits of heterotrimeric G proteins (Galpha) and acts as a guanine nucleotide dissociation inhibitor (GDI) for Galpha. Here we have investigated the interaction between Ngb and Galpha in more detail. We report that zebrafish Ngb, which shares about 50% amino acid sequence identity with human Ngb, does not have a GDI activity for Galpha. By carrying out exon swapping between zebrafish and human Ngb and site-directed mutagenesis, we have identified several residues that are crucial for the GDI activity of human Ngb.

Foldability, enzymatic activity, and interacting ability of barnase mutants obtained by permutation of secondary structure units

Barnase, a well-characterized ribonuclease, has been decomposed into six modules (M1-M6) or secondary structure units (S1-S6). We have studied the foldability and activity of the barnase mutants obtained by permutation of the four internal modules (M2-M5) or secondary structure units (S2-S5) to investigate whether permutation of these building blocks is a useful way to create foldable and/or functional proteins. In this study, we found that one of the secondary structure unit mutants was expressed in Escherichia coli only when His102 was substituted by alanine, which is a catalytic residue of wild-type barnase. This mutant (S2354H102A) had ordered conformations, which unfolded cooperatively during urea-induced unfolding experiments. S2354H102A interacted with other barnase mutants to show a distinct RNase activity, although its own activity was quite weak. This interaction was specific, because S2354H102A interacted with only barnase mutants having His 102 and certain orders of the secondary structure units giving a distinct RNase activity. These results suggest that secondary structure units permuted in barnase mutants maintain their intrinsic "interacting ability" that is used for the folding of wild-type barnase, and the units can form certain conformations that complement those of the appropriate counterparts. Seven of 23 secondary structure unit mutants and only 2 of 23 module mutants had RNase activity. On the basis of the results of analyses of foldability and RNase activity of the mutants performed in this and previous studies, we conclude that secondary structure units are more suitable than modules as building blocks to create novel foldable and/or functional proteins in the case of barnase.

Substitution of the heme binding module in hemoglobin alpha- and beta-subunits. Implication for different regulation mechanisms of the heme proximal structure between hemoglobin and myoglobin

In our previous work, we demonstrated that the replacement of the "heme binding module," a segment from F1 to G5 site, in myoglobin with that of hemoglobin alpha-subunit converted the heme proximal structure of myoglobin into the alpha-subunit type (Inaba, K., Ishimori, K. and Morishima, I. (1998) J. Mol. Biol. 283, 311-327). To further examine the structural regulation by the heme binding module in hemoglobin, we synthesized the betaalpha(HBM)-subunit, in which the heme binding module (HBM) of hemoglobin beta-subunit was replaced by that of hemoglobin alpha-subunit. Based on the gel chromatography, the betaalpha(HBM)-subunit was preferentially associated with the alpha-subunit to form a heterotetramer, alpha(2)[betaalpha(HBM)(2)], just as is native beta-subunit. Deoxy-alpha(2)[betaalpha(HBM)(2)] tetramer exhibited the hyperfine-shifted NMR resonance from the proximal histidyl N(delta)H proton and the resonance Raman band from the Fe-His vibrational mode at the same positions as native hemoglobin. Also, NMR spectra of carbonmonoxy and cyanomet alpha(2)[betaalpha(HBM)(2)] tetramer were quite similar to those of native hemoglobin. Consequently, the heme environmental structure of the betaalpha(HBM)-subunit in tetrameric alpha(2)[betaalpha(HBM)(2)] was similar to that of the beta-subunit in native tetrameric Hb A, and the structural conversion by the module substitution was not clear in the hemoglobin subunits. The contrastive structural effects of the module substitution on myoglobin and hemoglobin subunits strongly suggest different regulation mechanisms of the heme proximal structure between these two globins. Whereas the heme proximal structure of monomeric myoglobin is simply determined by the amino acid sequence of the heme binding module, that of tetrameric hemoglobin appears to be closely coupled to the subunit interactions.

The N-terminal region of the heme-regulated eIF2alpha kinase is an autonomous heme binding domain

The N-terminal domain (NTD) of the heme-regulated eukaryotic initiation factor (eIF)2alpha kinase (HRI) was aligned to sequences in the NCBI data base using ENTREZ and a PAM250 matrix. Significant similarity was found between amino acids 11-118 in the NTD of rabbit HRI and amino acids 16-120 in mammalian alpha-globins. Several conserved amino acid residues present in globins are conserved in the NTD of HRI. His83 of HRI was predicted to be equivalent to the proximal heme ligand (HisF8) that is conserved in all globins. Molecular modeling of the NTD indicated that its amino acid sequence was compatible with the globin fold. Recombinant NTD (residues 1-159) was expressed in Escherichia coli. Spectral analysis of affinity purified recombinant NTD indicated that the NTD contained stably bound hemin. Mutational analysis indicated that His83 played a critical structural role in the stable binding of heme to the NTD, and was required to stabilize full length HRI synthesized de novo in the rabbit reticulocyte lysate. These results indicate that the NTD of HRI is an autonomous heme-binding domain, with His83 possibly serving as the proximal heme binding ligand.

Crystal structure of a protein with an artificial exon-shuffling, module M4-substituted chimera hemoglobin beta alpha, at 2.5 A resolution

The crystal structure of the homotetramer of a chimera beta alpha-subunit of human hemoglobin was refined at 2.5 A resolution. The chimera subunit was constructed by replacing an exon-encoded module M4 of the beta-subunit with that of the alpha-subunit, simulating an exon-shuffling event. The implanted module M4 retained the native alpha-subunit structure, while module M3 was disturbed around the site where a new type of intron was recently found. Some of the residues were found in alternative conformations that avoid steric hindrance at the subunit interface. The modules are modestly rigid in their backbone structures by using side-chains to compensate for interface incompatibility.

Foldability of barnase mutants obtained by permutation of modules or secondary structure units

Modules, defined as stable, compact structure units in a globular protein, are good candidates for the construction of novel foldable proteins by permutation. Here we decomposed barnase into six modules (M1-M6) and constructed 23 barnase mutants containing permutations of the internal four (M2-M5) out of six modules. Globular proteins can also be subdivided into secondary structure units based on the extended structures that control the mutual relationships of the modules. We also decomposed barnase into six secondary structure units (S1-S6) and constructed 21 barnase mutants containing permutations of the internal four (S2-S5) out of six secondary structure units. Foldability of these two types of mutants was assessed by means of circular dichroism, fluorescence, and 1H-NMR measurements. A total of 15 of 23 module mutants and 15 of 21 secondary structure unit mutants formed definite secondary structures, such as alpha-helix and beta-sheet, at 20 microM owing to intermolecular interactions, but most of them converted to random coil structures at a lower concentration (1 microM). Of the 44 mutants, only two, M3245 and S2543, gave distinct near-UV CD spectra. S2543 especially showed definite signal dispersion in the amide and methyl regions of the 1H-NMR spectrum, though M3245 did not. Furthermore, urea-induced unfolding of S2543 monitored by far-UV CD and fluorescence measurements showed a distinct cooperative transition. These results strongly suggest that S2543 takes partially folded conformations in aqueous solution. Our results also suggest that building blocks such as secondary structure units capable of taking different stable conformations by adapting themselves to the surrounding environment, rather than building blocks such as modules having a specified stable conformation, are required for the formation of foldable proteins. Therefore, the use of secondary structure units for the construction of novel globular proteins is likely to be an effective approach.

Structural and functional roles of heme binding module in globin proteins: identification of the segment regulating the heme binding structure

To investigate structural and functional significance of a newly proposed structural unit in globins, the "heme binding module", we synthesized a "heme binding module"-substituted chimeric globin and characterized its function and structure. In our previous study we proposed that the heme binding module, corresponding to the segment from Leu(F1) to Phe(G5) in hemoglobin alpha-subunit, plays a key role in constructing the heme proximal structure in globins. The replacement of the heme binding module in myoglobin with that of hemoglobin alpha-subunit converted the absorption spectra into that of the alpha-subunit, and, in the resonance Raman spectra, the vibration mode characteristic of myoglobin completely disappeared after the module replacement. The hyperfine-shifted NMR resonances for the cyanide-bound form of the module-substituted myoglobin also revealed that the orientation of the axial histidine is close to that of the alpha-subunit rather than that of myoglobin, while the deviations of the resonance positions of the NMR signals from the amino acid residues located in the distal site were subtle, supporting the preferential structural alterations in the heme proximal site. The present finding for the structural alterations in the module-substituted myoglobin confirms that the heme binding module can be a segment regulating the heme proximal structure in globin proteins.

Design, construction, crystallization, and preliminary X-ray studies of a fine-tuning mutant (F133V) of module-substituted chimera hemoglobin

A chimera betaalpha-subunit of human hemoglobin was crystallized into a carbonmonoxy form. The protein was assembled by substituting the structural portion of a beta-subunit of hemoglobin (M4 module of the subunit) for its counterpart in the alpha-subunit. In order to overcome the inherent instability in the crystallization of the chimera subunit, a site-directed mutagenesis (F133V) technique was employed based on a computer model. The crystal was used for an X-ray diffraction study yielding a data set with a resolution of 2.5 A. The crystal belongs to the monoclinic space group P21, with cell dimensions of a = 62.9, b = 81.3, c = 55.1 A, and beta = 91.0 degrees . These dimensions are similar to the crystallographic parameters of the native beta-subunit tetramers in three different ligand states, one of which is a cyanide form that was also crystallized in this study.

Structural and functional effects of pseudo-module substitution in hemoglobin subunits. New structural and functional units in globin structure

Functional and structural significance of the "module" in proteins has been investigated for globin proteins. Our previous studies have revealed that some modules in globins are responsible for regulating the subunit association and heme environmental structures, whereas the module substitution often induces fatal structural destabilization, resulting in failure of functional regulation. In this paper, to gain further insight into functional and structural significance of the modular structure in globins, we focused upon the "pseudo-module" in globin structure where boundaries are located at the center of modules. Although the pseudo-module has been supposed not to retain a compactness, the betaalpha(PM3)-subunit, in which one of the pseudo-modules, the F1-H6 region, of the alpha-subunit is implanted into the beta-subunit, conserved stable globin structure, and its association property was converted into that of the alpha-subunit, as the case for the module substituted globin, the betaalpha(M4)-subunit. These results suggest that modules are not unique structural and functional units for globins. Interestingly, however, the recent reconsideration of the module boundary indicates that the modules in globins can be further divided into two small modules, and one of the boundaries for the new small modules coincides with that of the pseudo-module we substituted in this study. Although it would be premature to conclude the significance of the modular structure in globins, it can be safely said that we have found new structural units in globin structure, probably new modules.

'Module'-substituted globins: artificial exon shuffling among myoglobin, hemoglobin alpha- and beta-subunits

Based on the detailed structural analysis of proteins, Go [M. Go, Nature 291 (1981) 90-92] found that protein structures can be divided into some structural units, 'modules,' which correspond to peptides coded by exons. In the present study, to investigate functional and structural roles of modular structures in proteins, we have engineered eight chimera globins, in which the exons are shuffled among human myoglobin, human hemoglobin alpha- and beta-subunits, in addition to the chimera beta beta alpha-globin described previously [K. Wakasugi, K. Ishimori, K. Imai, Y. Wada, I. Morishima, J. Biol. Chem. 269 (1994) 18750-18756]. Although all of the chimera globins stoichiometrically bound the heme and their alpha-helical contents increased by heme incorporation as found for native globins, the alpha-helical contents of the chimera globins were significantly lower than those of native globins, suggesting that 'module' substitutions seriously affect the protein folding and stability in globins. The comparisons among several chimera globins demonstrated that such structural alterations are mainly attributed to loss of some key intermodular interactions for protein folding. By simultaneous substitution of the modules M1 and M4 from the same globin, the protein structure was stabilized, which indicates that the module packing between modules M1 and M4 would be one of the crucial interaction to stabilize the globin fold. Present results allow us to conclude that module substitutions would be available for designing and producing novel functional proteins if we can reproduce the stable modular packing in the 'module'-substituted proteins.