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Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core structure

Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core... IntroductionHaemoglobin, the protein responsible for oxygen transport in the human organism, is expected to satisfy a few conditions: (1) haemoglobin binds heme, which is the relatively large flat molecule with an iron atom in the central position; (2) the structure must be dynamic, as the biological process requires at least two stages – two conformations (R and T); and (3) haemoglobin represents the quaternary structure – two α-chains and two β-chains of a high very specific tetramer symmetry – shall be able to complex all these chains in a particular mutual orientation. Two chains (α and β) are very similar in the sense of a secondary structure (entirely helical forms); however, their folding is mutually dependent. The β-chain is not able to fold by itself, whereas the α-chain is. The α-chain is even treated as a specific chaperone for β-chain folding [1]. This relation is the object of the analysis presented in this paper.Haemoglobin has been the object of analysis for years, taking different aspects. Thus, the discussion of haemoglobin structure can be put in the context of protein-protein interaction. Complexation is the phenomenon of many faces. The presence of chemical compounds may influence complex formation [2]. Surface solvation is critical for protein-protein complexation [3]. Thermodynamic changes in the area of interface are accompanying early contacts of proteins [4], [5]. The influence of mutation in the interface is the object of analysis in Refs. [6], [7]. The dynamic forms especially in the interface area may influence the process of complexation [8].The heme binding mechanism is also critical for the recognition of heme binding by haemoglobin. The discussion of the binding of other hemes, which influence the enzymatic activity, is discussed in Ref. [9].The research of heme binding mechanism has its long history [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]. Recent research is focused on the large-scale modification of the target protein to bind heme [22]. The quaternary structure of haemoglobin, which is also the object of analysis presented in this paper, is discussed in Ref. [23]. Especially, the structural changes in the form of allosteric transitions are very important for haemoglobin activity [24].The characteristics of haemoglobin in the context of its hydrophobic core structure are discussed in this paper. The fuzzy oil drop model described in detail in many papers is applied to recognise the structural status of the hydrophobic core with respect to heme binding, the chain-chain complexation [25], [26].Because two forms of haemoglobin are discussed in this paper, we introduce the notation, making the distinguishing between structures easier. (AB)2 and (AB)1 denote complete four chain complexes (two α-chains and two β-chains) and the half of it (one α-chain and one β-chain), respectively. The structure of (AB)1 according to the discussion presented in Ref. [27] is treated as the intermediate product of the stepwise process of (AB)2 degradation. Significant structural changes with respect to heme stabilisation can be identified in comparison to the complete haemoglobin structure [28]. The loosing of heme discussed in Ref. [27] being seen in experiments as a process accompanied by a significant change of heme localisation in β-chain seems to be the important phenomenon from the point of view of haemoglobin degradation.The mechanism accompanying the dissociation of (AB)2 haemoglobin into (AB)1 is analysed in this paper, taking into account the structure of the hydrophobic core in each chain independently as well as in each discussed complex. The status of heme binding residues as well as residues involved in complexation is characterised by their participation in complex stability.The fuzzy oil drop model is able to quantitatively estimate the participation of residues engaged in the complexation in hydrophobic core formation [25], [26]. The stability of the hydrophobic core influences the stability of the entire complex.The status of the hydrophobic core is expressed in the fuzzy oil drop model using the relative distance (RD) parameter, which measures the RD between the idealised and observed distributions of hydrophobicity. The second reference distribution is the unified one deprived of any form of hydrophobicity differentiation. The high values of RD for the relations T-O-R (T for theoretical idealised distribution, O for observed, and R for unified with all residues representing equal hydrophobicity) suggest the high discordance between the expected and observed distributions. When this observation is being identified for the chain fragments engaged in the chain-chain interaction or for fragments engaged in heme binding, it suggests the significant influence on the protein structure by a chain complexed or a heme bound.The discussion based on this description will be used for the analysis of the status of the complex under consideration. It is expected that the changes of the hydrophobic core structure – treated as the factor expressing the tertiary structure stability – may clarify the status of heme binding in two discussed forms of haemoglobin.Materials and methodsDataTwo crystal structures are the object of analysis: (AB)2 1KD2 (PDB ID) [28] and (AB)1 3OO5 (PDB ID) [27].The complete complexes as well as each chain individually are analysed taking the structure of the hydrophobic core as criteria for the comparison.Fuzzy oil drop modelThis model has been described in many papers; however, the most detailed presentation of this model is given in Ref. [26]. The RD parameter is used to estimate the status of the hydrophobic core. An RD value above 0.5 is interpreted as a disordered hydrophobic core, whereas RD<0.5 suggests the presence of a regular core similar to the 3D Gauss function form of the hydrophobic core.The “Heme” position describes the status of residues engaged in heme binding. The “P-P” position describes the status of the interface – only residues engaged in the protein-protein interaction are taken under consideration. The “No-Heme” position describes the status of all residues not engaged in heme binding. The RD value is expected to specify to what extent the presence of heme influences the status of the hydrophobic core of the entire molecule. “No P-P” in analogy to “No-Heme” describes the status of the residues not engaged in P-P interaction. The interpretation of these values suggests the influence of the interface on the hydrophobic core in the molecule.ResultsThe set of parameters describing the complex and chains treated individually is presented in this part.Structure in complexThe profiles representing the relation between the expected and observed hydrophobicity distributions in both complexes are shown in Figures 1 and 2 for (AB)1 and (AB)2, respectively.Figure 1:Distribution of hydrophobicity in complexes in (AB)1.The positions or residues engaged in heme binding and complexation are denoted on the lower and upper axes, respectively.Figure 2:Distribution of hydrophobicity in complexes in (AB)2.The positions or residues engaged in heme binding and complexation are denoted on the lower and upper axes, respectively.The distribution of hydrophobicity in both dimers seems to be very similar. In all forms, the high hydrophobicity in the fragment 97–117 is expected; however, it is not observed. This high hydrophobicity is observed in the close neighborhood of residues engaged in the chain-chain complexation. The differences in this area are smaller in the (AB)1 complex. Probably, this discrepancy is caused by the engagement in the complex generation rather than in the monocentric core formation in (AB)2. As the RD parameter is chain length independent, it is possible to make the comparison of the status in different complexes.In Table 1, the status of the hydrophobic core of both discussed complexes is highly discordant with respect to the idealised structure of the hydrophobic core. The only exception is the status of residues engaged in P-P interaction in (AB)1. The interpretation of this observation suggests the higher relaxation (understood as a better fit to the idealised distribution) of the structure after the dissociation of one half of the complex resulting as a better fit of residues in the interface. The complexation of chains A and B in (AB)1 seems to be organised based on the generation appropriate for the complex organisation of the residues in the interface, which is probably not possible in (AB)2 complex. It also seems that the interface in (AB)2 is under constraints originated from the four-chain construction. On the contrary, the higher value of RD for (AB)1 for residues engaged in heme binding suggests that the status of the hydrophobic core in (AB)2 is less optimal from the point of view of heme binding. All other RD values are more or less comparable as shown in Figure 3.Table 1:RD parameters calculated for complexes (AB)1 and (AB)2, respectively.Dimer 3OO5 (AB)1Tetramer 1KD2 (AB)2Chain A0.6880.765Heme0.8000.746No L0.6700.760P-P0.4390.725No P-P0.6840.755Chain B0.6090.705Heme0.8000.742No L0.5930.700P-P0.5820.715No P-P0.5800.698“Heme” denotes the status of the residues engaged in heme binding. “No L” denotes the status of all residues not engaged in heme complexation. “P-P” denotes the status of residues engaged in protein-protein interaction. “No P-P” denotes the status of residues not engaged in P-P interaction. Boldfaced values distinguish the status discordant with respect to idealised distribution.Figure 3:Comparison of RD values for (AB)1 and (AB)2 complexes.The graphic form of the presentation of results is shown in Table 1.Structure of the individual chainsThe status of the individual chain in both discussed complexes is presented in Figures 4 and 5, where the expected hydrophobicity distribution can be compared to that observed in the individual chains. The status of the individual chain means that to calculate the value of RD the 3D Gauss function was generated for each chain individually.Figure 4:Distribution of hydrophobicity in complexes in (AB)1.Figure 5:Distribution of hydrophobicity in complexes in (AB)2.The RD values in Table 2 reveal the highly similar status of α-chains in both complexes. It is very well seen in Figure 6. The only differences can be seen in the β-chain. They concern the status of residues engaged in heme binding. The higher value is observed for the (AB)1 complex.Table 2:Comparison of RD parameters in the chains as they appear in the individual chains and complexes.(AB)1(AB)2ChainsIn dimerChainsIn tetramerChain A0.5190.6880.5250.765Heme0.5870.8000.6170.746No heme0.4890.6700.5070.760P-P0.5170.4390.5230.725No P-P0.5130.6840.5500.755Chain B0.4130.6090.4480.705Heme0.5570.8000.4760.742No L0.4010.5930.4280.700P-P0.6100.5820.5810.715No P-P0.3900.5800.2810.698Boldfaced values distinguish the status discordant with respect to idealised distribution.Figure 6:Change of the status in (AB)1 and (AB)2 chains treated as individual units.Conclusion and discussionThe analysis of the results shown in this paper point out the β-chain as more dependent on complexation. Generally, this chain represents a more relaxed form in (AB)1. It suggests that the release from the constraints originated in the four-chain complexation is not present. The difference is also the relation to the heme bound suggesting that the part not engaged in heme binding in the β-chain gets more relaxed in the sense of its own hydrophobic core formation in this chain.The recognition of the mechanism of heme binding and the behaviour of haemoglobin in its different forms are of special interest due to its high specificity and unique characteristics. However, generally the analysis of the specific activity of haemoglobin is of high importance with respect to drug design [29]. In this aspect, the research oriented on the general mechanism recognition plays a central role in biology and medicine-related disciplines [30], [31], [32].The results presented in this paper may give the input for the structural changes of hydrophobic core construction and its changes in haemoglobin. The hydrophobic core is not a frequent object of analysis. Therefore, the authors think that it may give an additional view of the commonly known phenomena.Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.Research funding: The work was financially supported by Jagiellonian University Medical College (Funder Id: 10.13039/100009045, grant systems K/ZDS/006363 and K/ZDS/006366).Employment or leadership: None declared.Honorarium: None declared.Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.References1.Vasseur C, Baudin-Creuza V. Role of alpha-hemoglobin molecular chaperone in the hemoglobin formation and clinical expression of some hemoglobinopathies. Transfus Clin Biol 2015;22:49–57.VasseurCBaudin-CreuzaVRole of alpha-hemoglobin molecular chaperone in the hemoglobin formation and clinical expression of some hemoglobinopathiesTransfus Clin Biol20152249572.Visscher KM, Kastritis PL, Bonvin AM. Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins 2015;83:445–58.VisscherKMKastritisPLBonvinAMNon-interacting surface solvation and dynamics in protein-protein interactionsProteins201583445583.Das A, Chakrabarti J, Ghosh M. Thermodynamics of interfacial changes in a protein-protein complex. Mol Biosyst 2014;10:437–45.DasAChakrabartiJGhoshMThermodynamics of interfacial changes in a protein-protein complexMol Biosyst201410437454.Yura K, Hayward S. The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics 2009;25:3108–13.YuraKHaywardSThe interwinding nature of protein-protein interfaces and its implication for protein complex formationBioinformatics2009253108135.Cameron DL, Jakus J, Pauleta SR, Pettigrew GW, Cooper A. Pressure perturbation calorimetry and the thermodynamics of noncovalent interactions in water: comparison of protein-protein. protein-heme. and cyclodextrin-adamantane complexes. J Phys Chem B 2010;114:16228–35.CameronDLJakusJPauletaSRPettigrewGWCooperAPressure perturbation calorimetry and the thermodynamics of noncovalent interactions in water: comparison of protein-protein. protein-heme. and cyclodextrin-adamantane complexesJ Phys Chem B201011416228356.Bougouffa S, Warwicker J. Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces. BMC Bioinformatics 2008;9:448.BougouffaSWarwickerJVolume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfacesBMC Bioinformatics200894487.Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005;102:15447–52.GuharoyMChakrabartiPConservation and relative importance of residues across protein-protein interfacesProc Natl Acad Sci USA200510215447528.Ehrlich LP, Nilges M, Wade RC. The impact of protein flexibility on protein-protein docking. Proteins 2005;58:126–33.EhrlichLPNilgesMWadeRCThe impact of protein flexibility on protein-protein dockingProteins200558126339.Nienhaus K, Hahn V, Hüpfel M, Nienhaus GU. Substrate binding primes human tryptophan 2,3-dioxygenase for heme binding. J Phys Chem B 2017;121:7412–20.NienhausKHahnVHüpfelMNienhausGUSubstrate binding primes human tryptophan 2,3-dioxygenase for heme bindingJ Phys Chem B201712174122010.Falk JE, Phillips JN, Perrin DD, O’Hagan JE. Binding of haem to protein in haemoglobin and myoglobin. Nature 1959;184:1651–2.FalkJEPhillipsJNPerrinDDO’HaganJEBinding of haem to protein in haemoglobin and myoglobinNature19591841651211.Keilin J. Nature of the haem-binding groups in native and denatured haemoglobin and myoglobin. Nature 1960;187:365–71.KeilinJNature of the haem-binding groups in native and denatured haemoglobin and myoglobinNature19601873657112.Benesch R. The molecular origin of the control mechanisms in haemoglobin. Bibl Haematol 1968;29:1049–55.BeneschRThe molecular origin of the control mechanisms in haemoglobinBibl Haematol19682910495513.Bunn HF, Jandl JH. Exchange of heme among hemoglobins and between haemoglobin and albumin. J Biol Chem 1968;243:465–75.BunnHFJandlJHExchange of heme among hemoglobins and between haemoglobin and albuminJ Biol Chem19682434657514.Krinsky MM, Alexander NM. Thyroid peroxidase. Nature of the heme binding to apoperoxidase. J Biol Chem 1971;246:4755–8.KrinskyMMAlexanderNMThyroid peroxidase. Nature of the heme binding to apoperoxidaseJ Biol Chem19712464755815.Nagel RL, Gibson QH, Jenkins T. Heme binding in haemoglobin J Capetown. J Mol Biol 1971;58:643–50.NagelRLGibsonQHJenkinsTHeme binding in haemoglobin J CapetownJ Mol Biol1971586435016.Uchida H, Heystek J, Klapper MH. Effect of structural perturbations on the heme-binding properties of human methemoglobin A. J Biol Chem 1971;246:6843–8.UchidaHHeystekJKlapperMHEffect of structural perturbations on the heme-binding properties of human methemoglobin AJ Biol Chem19712466843817.Gersonde K. Interaction between heme group and protein structure. Hamatol Bluttransfus 1972;10:183–90.GersondeKInteraction between heme group and protein structureHamatol Bluttransfus1972101839018.Fox JB Jr, Dymicky M, Wasserman AE. Heme-protein-heme interactions. Adv Exp Med Biol 1974;48:97–108.FoxJBJrDymickyMWassermanAEHeme-protein-heme interactionsAdv Exp Med Biol1974489710819.Caughey WS, Smythe GA, O’Keeffe DH, Maskasky JE, Smith MI. Heme A of cytochrome c oxidase. Structure and properties: comparisons with hemes B, C, and S and derivatives. J Biol Chem 1975;250:7602–22.CaugheyWSSmytheGAO’KeeffeDHMaskaskyJESmithMIHeme A of cytochrome c oxidase. Structure and properties: comparisons with hemes B, C, and S and derivativesJ Biol Chem197525076022220.Alberding N, Austin RH, Beeson KW, Chan SS, Eisenstein L, Frauenfelder H, et al. Tunneling in heme binding to heme proteins. Science 1976;192:1002–4.AlberdingNAustinRHBeesonKWChanSSEisensteinLFrauenfelderHTunneling in heme binding to heme proteinsScience19761921002421.Goddard WA 3rd, Olafson BD. Theoretical studies of oxygen binding. Ann N Y Acad Sci 1981;367:419–33.GoddardWA3rdOlafsonBDTheoretical studies of oxygen bindingAnn N Y Acad Sci19813674193322.Rai J. Mini heme-proteins: designability of structure and diversity of functions. Curr Protein Pept Sci 2017;18:1132–40.RaiJMini heme-proteins: designability of structure and diversity of functionsCurr Protein Pept Sci20171811324023.Lukin JA, Kontaxis G, Simplaceanu V, Yuan Y, Bax A, Ho C. Quaternary structure of hemoglobin in solution. Proc Natl Acad Sci USA 2003;100:517–20.LukinJAKontaxisGSimplaceanuVYuanYBaxAHoCQuaternary structure of hemoglobin in solutionProc Natl Acad Sci USA20031005172024.Swapna LS, Mahajan S, de Brevern AG, Srinivasan N. Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. BMC Struct Biol 2012;12:6.SwapnaLSMahajanSde BrevernAGSrinivasanNComparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteinsBMC Struct Biol201212625.Konieczny L, Brylinski M, Roterman I. Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol 2006;6:15–22.KoniecznyLBrylinskiMRotermanIGauss-function-based model of hydrophobicity density in proteinsIn Silico Biol20066152226.Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17:1477–507.KalinowskaBBanachMKoniecznyLRotermanIApplication of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteinsEntropy201517147750727.Yi J, Thomas LM, Musayev FN, Safo MK, Richter-Addo GB. Crystallographic trapping of heme loss intermediates during the nitrite-induced degradation of human haemoglobin. Biochemistry 2011;50:8323–32.YiJThomasLMMusayevFNSafoMKRichter-AddoGBCrystallographic trapping of heme loss intermediates during the nitrite-induced degradation of human haemoglobinBiochemistry20115083233228.Seixas FA, de Azevedo WF Jr, Colombo MF. Crystallization and x-ray diffraction data analysis of human deoxyhaemoglobin A(0) fully stripped of any anions. Acta Crystallogr D Biol Crystallogr 1999;55(Pt 11):1914–6.SeixasFAde AzevedoWFJrColomboMFCrystallization and x-ray diffraction data analysis of human deoxyhaemoglobin A(0) fully stripped of any anionsActa Crystallogr D Biol Crystallogr199955Pt 111914629.Brás NF, Fernandes PA, Ramos MJ. Discovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complex. Chem Biol Drug Des 2014;83:427–39.BrásNFFernandesPARamosMJDiscovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complexChem Biol Drug Des2014834273930.Bertonati C, Honig B, Alexov E. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J 2007;92:1891–9.BertonatiCHonigBAlexovEPoisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energiesBiophys J2007921891931.Bonet J, Caltabiano G, Khan AK, Johnston MA, Corbí C, Gómez A, et al. The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study. Proteins 2006;63:65–77.BonetJCaltabianoGKhanAKJohnstonMACorbíCGómezAThe role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational studyProteins200663657732.Schreiber G. Kinetic studies of protein-protein interactions. Curr Opin Struct Biol 2002;12:41–7.SchreiberGKinetic studies of protein-protein interactionsCurr Opin Struct Biol200212417 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bio-Algorithms and Med-Systems de Gruyter

Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core structure

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©2017 Walter de Gruyter GmbH, Berlin/Boston
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10.1515/bams-2017-0024
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Abstract

IntroductionHaemoglobin, the protein responsible for oxygen transport in the human organism, is expected to satisfy a few conditions: (1) haemoglobin binds heme, which is the relatively large flat molecule with an iron atom in the central position; (2) the structure must be dynamic, as the biological process requires at least two stages – two conformations (R and T); and (3) haemoglobin represents the quaternary structure – two α-chains and two β-chains of a high very specific tetramer symmetry – shall be able to complex all these chains in a particular mutual orientation. Two chains (α and β) are very similar in the sense of a secondary structure (entirely helical forms); however, their folding is mutually dependent. The β-chain is not able to fold by itself, whereas the α-chain is. The α-chain is even treated as a specific chaperone for β-chain folding [1]. This relation is the object of the analysis presented in this paper.Haemoglobin has been the object of analysis for years, taking different aspects. Thus, the discussion of haemoglobin structure can be put in the context of protein-protein interaction. Complexation is the phenomenon of many faces. The presence of chemical compounds may influence complex formation [2]. Surface solvation is critical for protein-protein complexation [3]. Thermodynamic changes in the area of interface are accompanying early contacts of proteins [4], [5]. The influence of mutation in the interface is the object of analysis in Refs. [6], [7]. The dynamic forms especially in the interface area may influence the process of complexation [8].The heme binding mechanism is also critical for the recognition of heme binding by haemoglobin. The discussion of the binding of other hemes, which influence the enzymatic activity, is discussed in Ref. [9].The research of heme binding mechanism has its long history [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]. Recent research is focused on the large-scale modification of the target protein to bind heme [22]. The quaternary structure of haemoglobin, which is also the object of analysis presented in this paper, is discussed in Ref. [23]. Especially, the structural changes in the form of allosteric transitions are very important for haemoglobin activity [24].The characteristics of haemoglobin in the context of its hydrophobic core structure are discussed in this paper. The fuzzy oil drop model described in detail in many papers is applied to recognise the structural status of the hydrophobic core with respect to heme binding, the chain-chain complexation [25], [26].Because two forms of haemoglobin are discussed in this paper, we introduce the notation, making the distinguishing between structures easier. (AB)2 and (AB)1 denote complete four chain complexes (two α-chains and two β-chains) and the half of it (one α-chain and one β-chain), respectively. The structure of (AB)1 according to the discussion presented in Ref. [27] is treated as the intermediate product of the stepwise process of (AB)2 degradation. Significant structural changes with respect to heme stabilisation can be identified in comparison to the complete haemoglobin structure [28]. The loosing of heme discussed in Ref. [27] being seen in experiments as a process accompanied by a significant change of heme localisation in β-chain seems to be the important phenomenon from the point of view of haemoglobin degradation.The mechanism accompanying the dissociation of (AB)2 haemoglobin into (AB)1 is analysed in this paper, taking into account the structure of the hydrophobic core in each chain independently as well as in each discussed complex. The status of heme binding residues as well as residues involved in complexation is characterised by their participation in complex stability.The fuzzy oil drop model is able to quantitatively estimate the participation of residues engaged in the complexation in hydrophobic core formation [25], [26]. The stability of the hydrophobic core influences the stability of the entire complex.The status of the hydrophobic core is expressed in the fuzzy oil drop model using the relative distance (RD) parameter, which measures the RD between the idealised and observed distributions of hydrophobicity. The second reference distribution is the unified one deprived of any form of hydrophobicity differentiation. The high values of RD for the relations T-O-R (T for theoretical idealised distribution, O for observed, and R for unified with all residues representing equal hydrophobicity) suggest the high discordance between the expected and observed distributions. When this observation is being identified for the chain fragments engaged in the chain-chain interaction or for fragments engaged in heme binding, it suggests the significant influence on the protein structure by a chain complexed or a heme bound.The discussion based on this description will be used for the analysis of the status of the complex under consideration. It is expected that the changes of the hydrophobic core structure – treated as the factor expressing the tertiary structure stability – may clarify the status of heme binding in two discussed forms of haemoglobin.Materials and methodsDataTwo crystal structures are the object of analysis: (AB)2 1KD2 (PDB ID) [28] and (AB)1 3OO5 (PDB ID) [27].The complete complexes as well as each chain individually are analysed taking the structure of the hydrophobic core as criteria for the comparison.Fuzzy oil drop modelThis model has been described in many papers; however, the most detailed presentation of this model is given in Ref. [26]. The RD parameter is used to estimate the status of the hydrophobic core. An RD value above 0.5 is interpreted as a disordered hydrophobic core, whereas RD<0.5 suggests the presence of a regular core similar to the 3D Gauss function form of the hydrophobic core.The “Heme” position describes the status of residues engaged in heme binding. The “P-P” position describes the status of the interface – only residues engaged in the protein-protein interaction are taken under consideration. The “No-Heme” position describes the status of all residues not engaged in heme binding. The RD value is expected to specify to what extent the presence of heme influences the status of the hydrophobic core of the entire molecule. “No P-P” in analogy to “No-Heme” describes the status of the residues not engaged in P-P interaction. The interpretation of these values suggests the influence of the interface on the hydrophobic core in the molecule.ResultsThe set of parameters describing the complex and chains treated individually is presented in this part.Structure in complexThe profiles representing the relation between the expected and observed hydrophobicity distributions in both complexes are shown in Figures 1 and 2 for (AB)1 and (AB)2, respectively.Figure 1:Distribution of hydrophobicity in complexes in (AB)1.The positions or residues engaged in heme binding and complexation are denoted on the lower and upper axes, respectively.Figure 2:Distribution of hydrophobicity in complexes in (AB)2.The positions or residues engaged in heme binding and complexation are denoted on the lower and upper axes, respectively.The distribution of hydrophobicity in both dimers seems to be very similar. In all forms, the high hydrophobicity in the fragment 97–117 is expected; however, it is not observed. This high hydrophobicity is observed in the close neighborhood of residues engaged in the chain-chain complexation. The differences in this area are smaller in the (AB)1 complex. Probably, this discrepancy is caused by the engagement in the complex generation rather than in the monocentric core formation in (AB)2. As the RD parameter is chain length independent, it is possible to make the comparison of the status in different complexes.In Table 1, the status of the hydrophobic core of both discussed complexes is highly discordant with respect to the idealised structure of the hydrophobic core. The only exception is the status of residues engaged in P-P interaction in (AB)1. The interpretation of this observation suggests the higher relaxation (understood as a better fit to the idealised distribution) of the structure after the dissociation of one half of the complex resulting as a better fit of residues in the interface. The complexation of chains A and B in (AB)1 seems to be organised based on the generation appropriate for the complex organisation of the residues in the interface, which is probably not possible in (AB)2 complex. It also seems that the interface in (AB)2 is under constraints originated from the four-chain construction. On the contrary, the higher value of RD for (AB)1 for residues engaged in heme binding suggests that the status of the hydrophobic core in (AB)2 is less optimal from the point of view of heme binding. All other RD values are more or less comparable as shown in Figure 3.Table 1:RD parameters calculated for complexes (AB)1 and (AB)2, respectively.Dimer 3OO5 (AB)1Tetramer 1KD2 (AB)2Chain A0.6880.765Heme0.8000.746No L0.6700.760P-P0.4390.725No P-P0.6840.755Chain B0.6090.705Heme0.8000.742No L0.5930.700P-P0.5820.715No P-P0.5800.698“Heme” denotes the status of the residues engaged in heme binding. “No L” denotes the status of all residues not engaged in heme complexation. “P-P” denotes the status of residues engaged in protein-protein interaction. “No P-P” denotes the status of residues not engaged in P-P interaction. Boldfaced values distinguish the status discordant with respect to idealised distribution.Figure 3:Comparison of RD values for (AB)1 and (AB)2 complexes.The graphic form of the presentation of results is shown in Table 1.Structure of the individual chainsThe status of the individual chain in both discussed complexes is presented in Figures 4 and 5, where the expected hydrophobicity distribution can be compared to that observed in the individual chains. The status of the individual chain means that to calculate the value of RD the 3D Gauss function was generated for each chain individually.Figure 4:Distribution of hydrophobicity in complexes in (AB)1.Figure 5:Distribution of hydrophobicity in complexes in (AB)2.The RD values in Table 2 reveal the highly similar status of α-chains in both complexes. It is very well seen in Figure 6. The only differences can be seen in the β-chain. They concern the status of residues engaged in heme binding. The higher value is observed for the (AB)1 complex.Table 2:Comparison of RD parameters in the chains as they appear in the individual chains and complexes.(AB)1(AB)2ChainsIn dimerChainsIn tetramerChain A0.5190.6880.5250.765Heme0.5870.8000.6170.746No heme0.4890.6700.5070.760P-P0.5170.4390.5230.725No P-P0.5130.6840.5500.755Chain B0.4130.6090.4480.705Heme0.5570.8000.4760.742No L0.4010.5930.4280.700P-P0.6100.5820.5810.715No P-P0.3900.5800.2810.698Boldfaced values distinguish the status discordant with respect to idealised distribution.Figure 6:Change of the status in (AB)1 and (AB)2 chains treated as individual units.Conclusion and discussionThe analysis of the results shown in this paper point out the β-chain as more dependent on complexation. Generally, this chain represents a more relaxed form in (AB)1. It suggests that the release from the constraints originated in the four-chain complexation is not present. The difference is also the relation to the heme bound suggesting that the part not engaged in heme binding in the β-chain gets more relaxed in the sense of its own hydrophobic core formation in this chain.The recognition of the mechanism of heme binding and the behaviour of haemoglobin in its different forms are of special interest due to its high specificity and unique characteristics. However, generally the analysis of the specific activity of haemoglobin is of high importance with respect to drug design [29]. In this aspect, the research oriented on the general mechanism recognition plays a central role in biology and medicine-related disciplines [30], [31], [32].The results presented in this paper may give the input for the structural changes of hydrophobic core construction and its changes in haemoglobin. The hydrophobic core is not a frequent object of analysis. Therefore, the authors think that it may give an additional view of the commonly known phenomena.Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.Research funding: The work was financially supported by Jagiellonian University Medical College (Funder Id: 10.13039/100009045, grant systems K/ZDS/006363 and K/ZDS/006366).Employment or leadership: None declared.Honorarium: None declared.Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.References1.Vasseur C, Baudin-Creuza V. Role of alpha-hemoglobin molecular chaperone in the hemoglobin formation and clinical expression of some hemoglobinopathies. Transfus Clin Biol 2015;22:49–57.VasseurCBaudin-CreuzaVRole of alpha-hemoglobin molecular chaperone in the hemoglobin formation and clinical expression of some hemoglobinopathiesTransfus Clin Biol20152249572.Visscher KM, Kastritis PL, Bonvin AM. Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins 2015;83:445–58.VisscherKMKastritisPLBonvinAMNon-interacting surface solvation and dynamics in protein-protein interactionsProteins201583445583.Das A, Chakrabarti J, Ghosh M. Thermodynamics of interfacial changes in a protein-protein complex. Mol Biosyst 2014;10:437–45.DasAChakrabartiJGhoshMThermodynamics of interfacial changes in a protein-protein complexMol Biosyst201410437454.Yura K, Hayward S. The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics 2009;25:3108–13.YuraKHaywardSThe interwinding nature of protein-protein interfaces and its implication for protein complex formationBioinformatics2009253108135.Cameron DL, Jakus J, Pauleta SR, Pettigrew GW, Cooper A. Pressure perturbation calorimetry and the thermodynamics of noncovalent interactions in water: comparison of protein-protein. protein-heme. and cyclodextrin-adamantane complexes. J Phys Chem B 2010;114:16228–35.CameronDLJakusJPauletaSRPettigrewGWCooperAPressure perturbation calorimetry and the thermodynamics of noncovalent interactions in water: comparison of protein-protein. protein-heme. and cyclodextrin-adamantane complexesJ Phys Chem B201011416228356.Bougouffa S, Warwicker J. Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces. BMC Bioinformatics 2008;9:448.BougouffaSWarwickerJVolume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfacesBMC Bioinformatics200894487.Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005;102:15447–52.GuharoyMChakrabartiPConservation and relative importance of residues across protein-protein interfacesProc Natl Acad Sci USA200510215447528.Ehrlich LP, Nilges M, Wade RC. The impact of protein flexibility on protein-protein docking. Proteins 2005;58:126–33.EhrlichLPNilgesMWadeRCThe impact of protein flexibility on protein-protein dockingProteins200558126339.Nienhaus K, Hahn V, Hüpfel M, Nienhaus GU. Substrate binding primes human tryptophan 2,3-dioxygenase for heme binding. J Phys Chem B 2017;121:7412–20.NienhausKHahnVHüpfelMNienhausGUSubstrate binding primes human tryptophan 2,3-dioxygenase for heme bindingJ Phys Chem B201712174122010.Falk JE, Phillips JN, Perrin DD, O’Hagan JE. Binding of haem to protein in haemoglobin and myoglobin. Nature 1959;184:1651–2.FalkJEPhillipsJNPerrinDDO’HaganJEBinding of haem to protein in haemoglobin and myoglobinNature19591841651211.Keilin J. Nature of the haem-binding groups in native and denatured haemoglobin and myoglobin. Nature 1960;187:365–71.KeilinJNature of the haem-binding groups in native and denatured haemoglobin and myoglobinNature19601873657112.Benesch R. The molecular origin of the control mechanisms in haemoglobin. Bibl Haematol 1968;29:1049–55.BeneschRThe molecular origin of the control mechanisms in haemoglobinBibl Haematol19682910495513.Bunn HF, Jandl JH. Exchange of heme among hemoglobins and between haemoglobin and albumin. J Biol Chem 1968;243:465–75.BunnHFJandlJHExchange of heme among hemoglobins and between haemoglobin and albuminJ Biol Chem19682434657514.Krinsky MM, Alexander NM. Thyroid peroxidase. Nature of the heme binding to apoperoxidase. J Biol Chem 1971;246:4755–8.KrinskyMMAlexanderNMThyroid peroxidase. Nature of the heme binding to apoperoxidaseJ Biol Chem19712464755815.Nagel RL, Gibson QH, Jenkins T. Heme binding in haemoglobin J Capetown. J Mol Biol 1971;58:643–50.NagelRLGibsonQHJenkinsTHeme binding in haemoglobin J CapetownJ Mol Biol1971586435016.Uchida H, Heystek J, Klapper MH. Effect of structural perturbations on the heme-binding properties of human methemoglobin A. J Biol Chem 1971;246:6843–8.UchidaHHeystekJKlapperMHEffect of structural perturbations on the heme-binding properties of human methemoglobin AJ Biol Chem19712466843817.Gersonde K. Interaction between heme group and protein structure. Hamatol Bluttransfus 1972;10:183–90.GersondeKInteraction between heme group and protein structureHamatol Bluttransfus1972101839018.Fox JB Jr, Dymicky M, Wasserman AE. Heme-protein-heme interactions. Adv Exp Med Biol 1974;48:97–108.FoxJBJrDymickyMWassermanAEHeme-protein-heme interactionsAdv Exp Med Biol1974489710819.Caughey WS, Smythe GA, O’Keeffe DH, Maskasky JE, Smith MI. Heme A of cytochrome c oxidase. Structure and properties: comparisons with hemes B, C, and S and derivatives. J Biol Chem 1975;250:7602–22.CaugheyWSSmytheGAO’KeeffeDHMaskaskyJESmithMIHeme A of cytochrome c oxidase. Structure and properties: comparisons with hemes B, C, and S and derivativesJ Biol Chem197525076022220.Alberding N, Austin RH, Beeson KW, Chan SS, Eisenstein L, Frauenfelder H, et al. Tunneling in heme binding to heme proteins. Science 1976;192:1002–4.AlberdingNAustinRHBeesonKWChanSSEisensteinLFrauenfelderHTunneling in heme binding to heme proteinsScience19761921002421.Goddard WA 3rd, Olafson BD. Theoretical studies of oxygen binding. Ann N Y Acad Sci 1981;367:419–33.GoddardWA3rdOlafsonBDTheoretical studies of oxygen bindingAnn N Y Acad Sci19813674193322.Rai J. Mini heme-proteins: designability of structure and diversity of functions. Curr Protein Pept Sci 2017;18:1132–40.RaiJMini heme-proteins: designability of structure and diversity of functionsCurr Protein Pept Sci20171811324023.Lukin JA, Kontaxis G, Simplaceanu V, Yuan Y, Bax A, Ho C. Quaternary structure of hemoglobin in solution. Proc Natl Acad Sci USA 2003;100:517–20.LukinJAKontaxisGSimplaceanuVYuanYBaxAHoCQuaternary structure of hemoglobin in solutionProc Natl Acad Sci USA20031005172024.Swapna LS, Mahajan S, de Brevern AG, Srinivasan N. Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. BMC Struct Biol 2012;12:6.SwapnaLSMahajanSde BrevernAGSrinivasanNComparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteinsBMC Struct Biol201212625.Konieczny L, Brylinski M, Roterman I. Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol 2006;6:15–22.KoniecznyLBrylinskiMRotermanIGauss-function-based model of hydrophobicity density in proteinsIn Silico Biol20066152226.Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17:1477–507.KalinowskaBBanachMKoniecznyLRotermanIApplication of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteinsEntropy201517147750727.Yi J, Thomas LM, Musayev FN, Safo MK, Richter-Addo GB. Crystallographic trapping of heme loss intermediates during the nitrite-induced degradation of human haemoglobin. Biochemistry 2011;50:8323–32.YiJThomasLMMusayevFNSafoMKRichter-AddoGBCrystallographic trapping of heme loss intermediates during the nitrite-induced degradation of human haemoglobinBiochemistry20115083233228.Seixas FA, de Azevedo WF Jr, Colombo MF. Crystallization and x-ray diffraction data analysis of human deoxyhaemoglobin A(0) fully stripped of any anions. Acta Crystallogr D Biol Crystallogr 1999;55(Pt 11):1914–6.SeixasFAde AzevedoWFJrColomboMFCrystallization and x-ray diffraction data analysis of human deoxyhaemoglobin A(0) fully stripped of any anionsActa Crystallogr D Biol Crystallogr199955Pt 111914629.Brás NF, Fernandes PA, Ramos MJ. Discovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complex. Chem Biol Drug Des 2014;83:427–39.BrásNFFernandesPARamosMJDiscovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complexChem Biol Drug Des2014834273930.Bertonati C, Honig B, Alexov E. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J 2007;92:1891–9.BertonatiCHonigBAlexovEPoisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energiesBiophys J2007921891931.Bonet J, Caltabiano G, Khan AK, Johnston MA, Corbí C, Gómez A, et al. The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study. Proteins 2006;63:65–77.BonetJCaltabianoGKhanAKJohnstonMACorbíCGómezAThe role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational studyProteins200663657732.Schreiber G. Kinetic studies of protein-protein interactions. Curr Opin Struct Biol 2002;12:41–7.SchreiberGKinetic studies of protein-protein interactionsCurr Opin Struct Biol200212417

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Bio-Algorithms and Med-Systemsde Gruyter

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