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1.
Sperm whale myoglobin was reconstituted with 1,4,5,8-tetramethylhemin. The hyperfine-shifted proton NMR signals from the prosthetic group exhibit remarkable pattern changes around 15 degrees C, while the globin resonances are normal to obey the Curie law. The NMR anomaly specifically observed for the heme signals suggests a slow to rapid rotational transition of the hemin about the iron-histidine bond. The temperature-dependent pattern changes were quantitatively analyzed by a dynamic NMR method. Two sets of analyses with the heme-methyl and pyrrole-proton lines consistently afforded delta H not equal to = 16.3 kcal/mol, delta S not equal to = 14.0 e.u., delta G not equal to = 12.1 kcal/mol at 298 K, and a frequency of 90 degrees heme rotation 5600 s-1 at 20 degrees C. The relatively large activation entropy suggests that structural rearrangements at the direct heme vicinity are involved and that efficient heme rotation is accomplished by a number of fluctuative local heme-globin contacts within a conserved crevice structure.  相似文献   

2.
Human apohemoglobin (globin) was spin-labeled at the beta-93 sulfhydryl groups with 2,2,5,5-tetramethyl-3-aminopyrrolidine-I-oxyl. Spin-labeled globin exhibited an EPR spectra that is less immobilized than that of spin-labeled hemoglobin, indicating the conformational difference in the vicinity of the label between hemoglobin and globin. Spectrophotometric titration of spin-labeled globin with protohemin showed that 1 mol of globin (on the tetramer basis) combines with 4 mol of hemin, producing a holomethemoglobin spectrophotometrically indistinguishable from native methemoglobin. The EPR spectrum was also changed strikingly upon the addition of protohemin. This change, however, was not proportional to the amount of hemin added, but marked changes occurred after 3 to 4 mol of hemin were mixed with 1 mol of spin-labeled globin. The EPR spectrum of spin-labeled hemoglobin thus prepared was identical with that prepared by direct spin labeling to methemoglobin. These results suggest the preferential binding of hemin to alpha-globin chains in the course of heme binding by globin. This assumption was further confirmed by preparing spin-labeled semihemoglobin in which only one kind of chain contained hemin (alpha h betaO SL and alpha O beta h SL). The EPR spectrum of the alpha h beta O SL molecule showed a slightly immobilized EPR spectrum, similar to that of spin-labeled globin mixed with 50% of the stoichiometric amount of hemin. On the other hand, the alpha O beta h SL molecule showed a distinctly different EPR signal from that of globin half-saturated with hemin, and showed an intermediate spectrum between those of beta h SL and alpha h beta h SL. These results indicate that heme binding to globin chains brings about a major conformational change in the protein moiety and that chain-chain association plays a secondary role. We conclude that hemin binds preferentially to alpha-globin chains and that the conformation of globin changes rapidly to that of methemoglobin after all four hemes are attached to globin heme pockets.  相似文献   

3.
To investigate the role of the heme axial ligand in the conformational stability of c-type cytochrome, we constructed M58C and M58H mutants of the red alga Porphyra yezoensis cytochrome c(6) in which the sixth heme iron ligand (Met58) was replaced with Cys and His residues, respectively. The Gibbs free energy change for unfolding of the M58H mutant in water (DeltaG degrees (unf)=1.48 kcal/mol) was lower than that of the wild-type (2.43 kcal/mol), possibly due to the steric effects of the mutation on the apoprotein structure. On the other hand, the M58C mutant exhibited a DeltaG degrees (unf) of 5.45 kcal/mol, a significant increase by 3.02 kcal/mol compared with that of wild-type. This increase was possibly responsible for the sixth heme axial bond of M58C mutant being more stable than that of wild-type according to the heme-bound denaturation curve. Based on these observations, we propose that the sixth heme axial ligand is an important key to determine the conformational stability of c-type cytochromes, and the sixth Cys heme ligand will give stabilizing effects.  相似文献   

4.
New understanding of the engineering and allosteric regulation of natural protein conformational switches (such as those that couple chemical and ionic signals, mechanical force, and electro/chemical free energy for biochemical activation, catalysis, and motion) can be derived from simple de novo designed synthetic protein models (maquettes). We demonstrate proof of principle of both reversible switch action and allosteric regulation in a tetra-alpha-helical bundle protein composed of two identical di-helical subunits containing heme coordinated at a specific position close to the disulfide loop region. Individual bundles assume one of two switch states related by large-scale mechanical changes: a syn-topology (helices of the different subunits parallel) or anti-topology (helices antiparallel). Both the spectral properties of a coproporphyrin probe appended to the loop region and the distance-dependent redox interaction between the hemes identify the topologies. Beginning from a syn-topology, introduction of ferric heme in each subunit (either binding or redox change) shifts the topological balance by 25-50-fold (1.9-2.3 kcal/mol) to an anti-dominance. Charge repulsion between the two internal cationic ferric hemes drives the syn- to anti-switch, as demonstrated in two ways. When fixed in the syn-topology, the second ferric heme binding is 25-80-fold (1.9-2.6 kcal/mol) weaker than the first, and adjacent heme redox potentials are split by 80 mV (1.85 kcal/mol), values that energetically match the shift in topological balance. Allosteric and cooperative regulation of the switch by ionic strength exploits the shielded charge interactions between the two hemes and the exposed, cooperative interactions between the coproporphyrin carboxylates.  相似文献   

5.
Dynamic properties of deoxymyoglobin are studied theoretically by the analysis of conformational fluctuations. Root-mean-square atomic fluctuations and distance fluctuations between different segments reveal the mechanical construction of the molecule. Eight alpha-helices behave as relatively rigid bodies and corner regions are more flexible, showing larger fluctuations. More particularly, corner regions EF and GH are specific in that flanking alpha-helices extend their rigidity up to a point in the corner region and the two rigid segments are connected flexibly at that point. The FG corner is exceptional. A segment from the F helix to the beginning of the G helix, in which the FG corner is included, becomes relatively rigid by means of strong interactions with the heme group. The whole myoglobin molecule is divided into two large units of motion, one extending from the B to the E helix, and the other from the F to the H helix. These two units are connected covalently by the EF corner. However, dynamic interactions between these two units take place mainly through contacts between helices B and G and not through the EF corner. From correlation coefficients between fluctuational motions of residues and the heme group, 55 residues are identified as having strong dynamic interactions with the heme moiety. Among them, 18 residues in the three segments, one consisting of residues from the C helix to the CD corner, a second consisting of the E helix, and a third from the F helix to the beginning of the G helix, are in close contact with the heme group. Twenty-two of the 55 residues are within four residues of the 18 residues in their sequential residue number and are more than 3 A away from the heme group. The other 15 residues are located further in the sequential residue number and are all found in helices A and H. They are more than 6 A away from the heme group. By the use of correlation coefficients of fluctuations between residues, it is found that dynamic interaction with the heme group is transmitted to the A helix and the beginning of the H helix in the direction Leu(E15)----[Val(All) and Trp(A12)]. The transmission to the C-terminal end of the H helix is mediated by a long segment, from the end of the EF corner to the beginning of the G helix, that lies on the heme group and has close contacts over a wide range.(ABSTRACT TRUNCATED AT 400 WORDS)  相似文献   

6.
A 150 picosecond molecular dynamics computer simulation of the C-terminal fragment of the L7/L12 ribosomal protein from Escherichia coli is reported. The molecular dynamics results are compared with the available high-resolution X-ray data in terms of atomic positions, distances and positional fluctuations. Good agreement is found between the molecular dynamics results and the X-ray data. The form and parameters of the interaction potential energy function and the procedures for deriving it are discussed. Some current misunderstandings concerning the ways of evaluating the efficiency of molecular dynamics algorithms and of application of bond-length constraints in protein simulations are cleared up. The 150 picosecond trajectory has been scanned in a search for correlated motions within and between secondary structure elements. The beta-strands have diffusional stretching modes, and uncorrelated transversal displacements. The dynamic analysis of alpha-helices shows a variety of features. The atomic fluctuations differ between the helix ends; this effect reflects long time-scale motions. Two alpha-helices, alpha A and alpha C, show diffusive longitudinal stretching modes. The third helix, alpha B, has a correlated asymmetric longitudinal stretching; the N-terminal part dominates this behaviour. Furthermore, alpha B presents a librational motion with respect to the other parts of the molecule with a frequency of approximately 5 cm-1. This motion is coupled to helix stretching. Interestingly, the regions of highly conserved residues contain the most mobile parts of the molecule.  相似文献   

7.
The unique feature of this model is that both the fractional saturation and the free energy change are handled within the framework of the tension-displacement mechanism for hemoglobin co-operativity proposed by Perutz (1970, 1972), i.e. heme iron movement and associated changes in the protein globin internal tension, tau. Physically, tau is the force applied by the protein globin on the proximal histidine, preventing the iron stereochemistry from attaining the geometry preferred in the bound state. It is assumed that a change in position of the heme iron on ligand binding displaces the protein globin proportionately, thereby decreasing tau at neighboring sites; the resulting energy change is assumed to be delocalized throughout the flexible protein globin rather than localized at the heme group per se. The physical interpretation of the model parameters has important implications with regard to data analysis: first, structural data is used to fix the molecular displacements lt and lr; second, jt/jr provides a measure of the protein's intrinsic (i.e. tau = 0) affinity for the bound ligand, and third the set [Ei] is a property of the hemoglobin molecule only and can be determined, in principle, using structural data and optical absorption spectra. The calculated protein globin internal tension in the tense, unbound state (approximately 2 X 10(-5) dyne), determined from the fractional saturation data of Joels & Pugh (1958), is very similar (approximately 3.2 X 10(-5) dyne) to the value estimated by Hopfield (1973) from free energy considerations.  相似文献   

8.
L Richard  L Genberg  J Deak  H L Chiu  R J Miller 《Biochemistry》1992,31(44):10703-10715
Phase grating spectroscopy has been used to follow the optically triggered tertiary structural changes of carboxymyoglobin (MbCO) and carboxyhemoglobin (HbCO). Probe wavelength and temperature dependencies have shown that the grating signal arises from nonthermal density changes induced by the protein structural changes. The material displaced through the protein structural changes leads to the excitation of coherent acoustic modes of the surrounding water. The coupling of the structural changes to the fluid hydrodynamics demonstrates that a global change in the protein structure is occurring in less than 30 ps. The global relaxation is on the same time scale as the local changes in structure in the vicinity of the heme pocket. The observed dynamics for global relaxation and correspondence between the local and global structural changes provides evidence for the involvement of collective modes in the propagation of the initial tertiary conformational changes. The energetics can also be derived from the acoustic signal. For MbCO, the photodissociation process is endothermic by 21 +/- 2 kcal/mol, which corresponds closely to the expected Fe-CO bond enthalpy. In contrast, HbCO dissipates approximately 10 kcal/mol more energy relative to myoglobin during its initial tertiary structural relaxation. The difference in energetics indicates that significantly more energy is stored in the hemoglobin structure and is believed to be related to the quaternary structure of hemoglobin not present in the monomeric form of myoglobin. These findings provide new insight into the biomechanics of conformational changes in proteins and lend support to theoretical models invoking stored strain energy as the driving force for large amplitude correlated motions.  相似文献   

9.
The potential of mean force for Na+ and K+ ions as a function of position in the interior of a periodic poly(L,D)-alanine model for the gramicidin beta-helix is calculated with a detailed atomic model and realistic interactions. The calculated free energy barriers are 4.5 kcal/mol for Na+ and 1.0 kcal/mol for K+. A decomposition of the free energy demonstrates that the water molecules make a significant contribution to the free energy of activation. There is an increase in entropy at the transition state associated with greater fluctuations. Analysis reveals that the free energy profile of ions in the periodic channel is controlled not by the large interaction energy involving the ion but rather by the weaker water-water, water-peptide and peptide-peptide hydrogen bond interactions. The interior of the channel retains much of the solvation properties of a liquid in its interactions with the cations. Of particular importance is the flexibility of the helix, which permits it to respond to the presence of an ion in a fluidlike manner. The distortion of the helix is local (limited to a few carbonyls) because the structure is too flexible to transmit a perturbation to large distances. The plasticity of the structure (i.e., the property to deform without generating a large energy stress) appears to be an essential factor in the transport of ions, suggesting that a rigid helix model would be inappropriate.  相似文献   

10.
Hemopexin is a serum glycoprotein that binds heme with high affinity and delivers heme to the liver cells via receptor-mediated endocytosis. A hinge region connects the two non-disulfide-linked domains of hemopexin, a 35-kDa N-terminal domain (domain I) that binds heme, and a 25-kDa C-terminal domain (domain II). Although domain II does not bind heme, it assumes one structural state in apo-hemopexin and another in heme-hemopexin, and this change is important in facilitating the association of heme-hemopexin with its receptor. In order to elucidate the structure and function of hemopexin, it is important to understand how structural information is transmitted to domain II when domain I binds heme. Here we report a study of the protein-protein interactions between domain I and domain II using analytical ultracentrifugation and isothermal titration calorimetry. Sedimentation equilibrium analysis showed that domain I associates with domain II both in the presence and absence of heme with Kd values of 0.8 microM and 55 microM, respectively. The interaction between heme-domain I and domain II has a calorimetric enthalpy of +11 kcal/mol, a heat capacity (delta Cp) of -720 cal/mol.K, and a calculated entropy of +65 cal/mol.K. By varying the temperature of the centrifugation equilibrium runs, a van't Hoff plot with an apparent change in enthalpy (delta H) of -3.6 kcal/mol and change in entropy (delta S) of +8.1 cal/mol.K for the association of apo-domain I with domain II was obtained.(ABSTRACT TRUNCATED AT 250 WORDS)  相似文献   

11.
Quaternary-transformation-induced changes at the heme in deoxyhemoglobins   总被引:4,自引:0,他引:4  
Quaternary-structure-induced differences in both the high- and low-frequency regions of the resonance Raman spectrum of the heme have been detected in a variety of hemoglobins. These differences may be the result of (1) changes in the amino acid sequence, induced by genetic and chemical modifications, and (2) alterations in the quaternary structure. For samples in solution in low ionic strength buffers, differences in the 1357-cm-1 line (an electron-density-sensitive vibrational mode) correlate with differences in the 216-cm-1 line (the iron-histidine stretching mode). Thus, changes in the iron-histidine bond and changes in the pi-electron density of the porphyrin depend upon a common heme-globin interaction. The quaternary-structure-induced changes in the vibrational modes associated with the heme demonstrate that there is extensive communication between the heme and the globin and impact on models for the energetics of cooperativity. The local interactions of the iron-histidine mode are energetically small and destabilize the deoxy heme in the T structure with respect to the R structure. Therefore, these interactions must be larger in the ligated protein than in the deoxy protein to obtain a negative free energy of cooperativity. Additionally, our data imply that the deprotonation of the proximal histidine does not play a major role in the energetics of cooperativity. On the other hand, models for cooperativity that require conformational changes in the iron-histidine bond or direct interaction between the porphyrin and the protein are qualitatively consistent with the observed variation of heme electronic structure in concert with protein quaternary structure.  相似文献   

12.
Glutamate dehydrogenase from Candida utilis undergoes a reversible conformational transition between an active and an inactive state at low pH AND low temperature. This conformational transition can also be followed by fluorescence measurements. The temperature-dependent equilibrium between the active and the inactive state is characterized by a transition temperature of 10.7 degrees C and a delta H value of 148 kcal/mol (620 kJ/mol). The temperature dependence of the enzymic activity above 15 degrees C yields an activation energy of 15 kcal/mol (63 kJ/mol), a larger value than that for the beef liver enzyme (9 kcal/mol; 38 kJ/mol). In contrast to the yeast enzyme the Arrhenius plot is linear and, therefore, the beef liver enzyme is not transformed into an inactive conformation at low temperatures. Sedimentation analysis shows that the inactivation of the Candida utilis enzyme is not caused by change in the quaternary structure. The pH dependence of the conformational transition at low pH measured by fluorescence change is characterized by a pK value of 7.01 for the enzyme in the absence and of 6.89 for the enzyme in the presence of 2-oxoglutarate with a Hill coefficient of 3.4 in both cases. Similar results are found when the pH dependence of the enzymic activity is analyzed. With the beef liver enzyme the same pK value is obtained but with a Hill coefficient of 1 indicating cooperativity only in the case of the Candida utilis enzyme. The best fit of the pH dependence of the rate constants of the fluorescence changes was obtained with pK values of 7.45 and 6.45 for the active and the inactive state respectively. In this model the lowest time constant which is obtained at the pH of the equilibrium was found to be 0.05 s-1. Preincubation experiments with the substrate 2-oxoglutarate but not with the coenzyme shift the equilibrium to the active conformation. The coenzyme obviously reduces the rate constant of the conformational transition. The sedimentation coefficient (SO20, w) and the molecular weight were found to be 11.0 S and 276 000, respectively. The enzyme molecule is built up by six polypeptide chains each having a molecular weight of 47 000.  相似文献   

13.
S-nitrosylation-induced conformational change in blackfin tuna myoglobin   总被引:1,自引:0,他引:1  
S-nitrosylation is a post-translational protein modification that can alter the function of a variety of proteins. Despite the growing wealth of information that this modification may have important functional consequences, little is known about the structure of the moiety or its effect on protein tertiary structure. Here we report high-resolution x-ray crystal structures of S-nitrosylated and unmodified blackfin tuna myoglobin, which demonstrate that in vitro S-nitrosylation of this protein at the surface-exposed Cys-10 directly causes a reversible conformational change by "wedging" apart a helix and loop. Furthermore, we have demonstrated in solution and in a single crystal that reduction of the S-nitrosylated myoglobin with dithionite results in NO cleavage from the sulfur of Cys-10 and rebinding to the reduced heme iron, showing the reversibility of both the modification and the conformational changes. Finally, we report the 0.95-A structure of ferrous nitrosyl myoglobin, which provides an accurate structural view of the NO coordination geometry in the context of a globin heme pocket.  相似文献   

14.
The interaction of hemoglobin with phosphatidylserine vesicles at low ionic strength and pH conditions was studied. The fluorescence intensity of a lipid embedded probe was quenched by bound Hb but could not be reversed by an elevation of ionic strength and pH. The irreversibility of the fluorescence quenching is a time-dependent process associated with changes in the heme Soret and visible spectra. The rate of these changes was much faster for methemoglobin than for either cyanomethemoglobin or oxyhemoglobin. Elevation of ionic strength released out of the bound hemoglobin into the water phase most of the globin but only a small fraction of the heme. The data are interpreted as demonstrating the ability of phosphatidylserine vesicles to compete with globin for the heme group. When Hb binds to the liposome, heme is being transferred into the lipid phase and the rate-limiting step is the dissociation of the heme-globin complex. The fact that binding of heme to the lipid vesicles is very strong was demonstrated by the failure of hemin to interact with globin when the two were rapidly mixed in the presence of phosphatidylserine vesicles. A multi-step process is suggested to explain the results of Hb phosphatidylserine interaction.  相似文献   

15.
The free energy of binding of a ligand to a macromolecule is here formally decomposed into the (effective) energy of interaction, reorganization energy of the ligand and the macromolecule, conformational entropy change of the ligand and the macromolecule, and translational and rotational entropy loss of the ligand. Molecular dynamics simulations with implicit solvation are used to evaluate these contributions in the binding of biotin, biotin analogs, and two peptides to avidin and streptavidin. We find that the largest contribution opposing binding is the protein reorganization energy, which is calculated to be from 10 to 30 kcal/mol for the ligands considered here. The ligand reorganization energy is also significant for flexible ligands. The translational/rotational entropy is 4.5-6 kcal/mol at 1 M standard state and room temperature. The calculated binding free energies are in the correct range, but the large statistical uncertainty in the protein reorganization energy precludes precise predictions. For some complexes, the simulations show multiple binding modes, different from the one observed in the crystal structure. This finding is probably due to deficiencies in the force field but may also reflect considerable ligand flexibility.  相似文献   

16.
The resonance Raman spectra of cytochrome c oxidase in protonated buffer compared to that in deuterated buffer indicate that water molecules are near the heme of cytochrome a. Differences in widths of the heme line at 1610 cm-1, after short exposure to D2O, and, additionally, of the heme line at 1625 cm-1, after long exposure, can be accounted for by changes in resonance vibrational energy transfer between modes of cytochrome a2+ and the bending mode of water molecules in the heme pocket. On the basis of the assignment of these modes, we place one water molecule near the vinyl group and one water molecule near the formyl group of the cytochrome a heme. These water molecules may play several possible functional roles.  相似文献   

17.
In this study, the thermodynamic properties of substrate-ribozyme recognition were explored using a system derived from group II intron ai5gamma. Substrate recognition by group II intron ribozymes is of interest because any nucleic ac?id sequence can be targeted, the recognition sequence can be quite long (>/=13 bp), and reaction can proceed with a very high degree of sequence specificity. Group II introns target their substrates throug?h the formation of base-pairing interactions with two regions of the intron (EBS1 and EBS2), which are usually located far apart in the secondary structure. These structures pair with adjacent, corresponding sites (IBS1 and IBS2) on the substrate. In order to understand the relative energetic contribution of each base-pairing interaction (EBS1-IBS1 or EBS2-IBS2) to substrate binding energy, the free energy of each helix was measured. The individual helices were found to have base-pairing free energies similar to those calculated for regular RNA duplexes of the same sequence, suggesting that each recognition helix derives its binding energy from base-pairing interactions alone and that each helix can form independently. Most interestingly, it was found that the sum of the measured individual free energies (approximately 20 kcal/mol) was much higher than the known free energy for substrate binding (approximately 12 kcal/mol). This indicates that certain group II intron ribozymes can bind their substrates in an antagonistic fashion, paying a net energetic penalty upon binding the full-length substrate. This loss of binding energy is not due to weakening of individual helices, but appears to be linked to ribozyme conformational changes induced by substrate binding. This coupling between substrate binding and ribozyme conformational rearrangement may provide a mechanism for lowering overall substrate binding energy while retaining the full information content of 13 bp, thus resulting in a mechanism for ensuring sequence specificity.  相似文献   

18.
The conformational stability and flexibility of insulin containing a cross-link between the alpha-amino group of the A-chain to the epsilon-amino group of Lys29 of the B-chain was examined. The cross-link varied in length from 2 to 12 carbon atoms. The conformational stability was determined by guanidine hydrochloride-induced equilibrium denaturation and flexibility was assessed by H2O/D2O amide exchange. The cross-link has substantial effects on both conformational stability and flexibility which depend on its length. In general, the addition of a cross-link enhances conformational stability and decreases flexibility. The optimal length for enhanced stability and decreased flexibility was the 6-carbon link. For the 6-carbon link the Gibbs free energy of unfolding was 8.0 kcal/mol compared to 4.5 kcal/mol for insulin, and the amide exchange rate decreased by at least 3-fold. A very short cross-link (i.e. the 2-carbon link) caused conformational strain that was detectable by a lack of stabilization in the Gibbs free energy of unfolding and enhancement in the amide exchange rate compared to insulin. The effect of the cross-link length on insulin hydrodynamic properties is discussed relative to previously obtained receptor binding results.  相似文献   

19.
A semi-empirical conformational analysis is used to compute the conformation of (+)-propranolol inserted in dipalmitoylphosphatidylcholine. In a first step, the minimal conformational energy of the isolated molecule at the hydrocarbon-water interface is calculated as the sum of the contributions resulting from the Van der Waals, the torsional, the electrostatic and the transfer energies. Five pairs of conformers of minimal energy are determined. They are compared to data available from other experimental approaches. In a second step, they are assembled with dipalmitoylphosphatidylcholine at the interface. Although propranolol is considered in its protonated form, the electrostatic interaction with dipalmitoylphosphatidylcholine is negligible as compared to the Van der Waals interaction. The area occupied per propranolol molecule is between 0.53 and 0.64 nm2/molecule. In the most probable modes of insertion of propranolol into the lipid layer, the naphthyl moiety of the compound interacts with the lipid acyl chains. The protonated amino group is located in the vicinity of the phosphate residue possibly causing an electrostatic interaction.  相似文献   

20.
We have investigated the potential use of differential scanning calorimetry (DSC) to characterize conformational changes in proteins with emphasis on a conformational change in the myosin head which may be related to the power-stroke providing force production in muscle contraction. Simulations indicate that two-state conformational transitions with enthalpy changes greater than approximately 30 kcal/mol should be observable by DSC. We present here differential scanning calorimetric studies of a predenaturation structural change in heavy meromyosin. The high concentration of protein required for these experiments leads to potential contributions from intermolecular interactions. The technical difficulties associated with studying conformational transitions by DSC are discussed.  相似文献   

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