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1.
PLoS One ; 17(12): e0278417, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36454779

RESUMO

The mechanism underlying allostery in hemoglobin (Hb) is still not completely understood. Various models describing the action of allosteric effectors on Hb function have been published in the literature. It has also been reported that some allosteric effectors-such as chloride ions, inositol hexaphosphate, 2,3-diphospho-glycerate and bezafibrate-considerably lower the oxygen affinity of Hb. In this context, an important question is the extent to which these changes influence the conformational dynamics of the protein. Earlier, we elaborated a challenging method based on phosphorescence quenching, which makes characterizing protein-internal dynamics possible in the ms time range. The experimental technique involves phosphorescence lifetime measurements in thermal equilibrium at varied temperatures from 10 K up to 273 K, based on the signal of Zn-protoporphyrin substituted for the heme in the ß-subunits of Hb. The thermal activation of protein dynamics was observed by the enhancement of phosphorescence quenching attributed to O2 diffusion. It was shown that the thermal activation of protein matrix dynamics was clearly distinguishable from the dynamic activation of the aqueous solvent, and was therefore highly specific for the protein. In the present work, the same method was used to study the changes in the parameters of the dynamic activation of human HbA induced by binding allosteric effectors. We interpreted the phenomenon as phase transition between two states. The fitting of this model to lifetime data yielded the change of energy and entropy in the activation process and the quenching rate in the dynamically activated state. The fitted parameters were particularly sensitive to the presence of allosteric effectors and could be interpreted in line with results from earlier experimental studies. The results suggest that allosteric effectors are tightly coupled to the dynamics of the whole protein, and thus underline the importance of global dynamics in the regulation of Hb function.


Assuntos
Hemoglobina A , Radiação , Humanos , Bezafibrato , Entropia , Heme
2.
PLoS One ; 13(3): e0194994, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29584765

RESUMO

The general question by what mechanism an "effector" molecule and the hemes of hemoglobin interact over widely separated intramolecular distances to change the oxygen affinity has been extensively investigated, and still has remained of central interest. In the present work we were interested in clarifying the general role of the protein matrix and its dynamics in the regulation of human adult hemoglobin (HbA). We used a spectroscopy approach that yields the compressibility (κ) of the protein matrix around the hemes of the subunits in HbA and studied how the binding of heterotropic allosteric effectors modify this parameter. κ is directly related to the variance of volume fluctuation, therefore it characterizes the molecular dynamics of the protein structure. For the experiments the heme groups either in the α or in the ß subunits of HbA were replaced by fluorescent Zn-protoporphyrinIX, and series of fluorescence line narrowed spectra were measured at varied pressures. The evaluation of the spectra yielded the compressibility that showed significant dynamic asymmetry between the subunits: κ of the α subunit was 0.17±0.05/GPa, while for the ß subunit it was much higher, 0.36±0.07/GPa. The heterotropic effectors, chloride ions, inositol hexaphosphate and bezafibrate did not cause significant changes in κ of the α subunits, while in the ß subunits the effectors lead to a significant reduction down to 0.15±0.04/GPa. We relate our results to structural data, to results of recent functional studies and to those of molecular dynamics simulations, and find good agreements. The observed asymmetry in the flexibility suggests a distinct role of the subunits in the regulation of Hb that results in the observed changes of the oxygen binding capability.


Assuntos
Hemoglobinas/metabolismo , Regulação Alostérica , Sequência de Aminoácidos , Sítios de Ligação , Corantes Fluorescentes/química , Hemoglobinas/química , Humanos , Simulação de Dinâmica Molecular , Oxigênio/química , Oxigênio/metabolismo , Ligação Proteica , Estrutura Quaternária de Proteína , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , Alinhamento de Sequência , Espectrometria de Fluorescência
3.
J Phys Chem B ; 120(9): 2165-78, 2016 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-26890079

RESUMO

Construction of the presynaptic filament (PSF) of proper helical structure by Rad51 recombinases is a prerequisite of the progress of homologous recombination repair. We studied the contribution of ATP-binding to this structure of wt human Rad51 (hRad51). We exploited the protein-dissociation effect of high hydrostatic pressure to determine the free energy of dissociation of the protomer interfaces in hRad51 oligomer states and used electron microscopy to obtain topological parameters. Without cofactors ATP and Ca(2+) and template DNA, hRad51 did not exist in monomer form, but it formed rodlike long filaments without helical order. ΔG(diss) indicated a strong inherent tendency of aggregation. Binding solely ssDNA left the filament unstructured with slightly increased ΔG(diss). Adding only ATP and Ca(2+) to the buffer disintegrated the self-associated rods into rings and short helices of further increased ΔG(diss). Rad51 binding to ssDNA only with ATP and Ca bound could lead to ordered helical filament formation of proper pitch size with interface contacts of K(d) ∼ 2 × 10(-11) M, indicating a structure of outstanding stability. ATP/Ca binding increased the ΔG(diss) of protomer contacts in the filament by 16 kJ/mol. The results emphasize that ATP-binding in the PSF of hRad51 has an essential, yet purely structural, role.


Assuntos
Trifosfato de Adenosina/metabolismo , DNA de Cadeia Simples/metabolismo , Rad51 Recombinase/metabolismo , Humanos , Microscopia Eletrônica de Transmissão , Ligação Proteica , Espectrometria de Fluorescência
4.
Biophys J ; 104(3): 677-82, 2013 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-23442918

RESUMO

Protein function is governed by the underlying conformational dynamics of the molecule. The experimental and theoretical work leading to contemporary understanding of enzyme dynamics was mostly restricted to the large-scale movements of single-domain proteins. Collective movements resulting from a regulatory interplay between protein domains is often crucial for enzymatic activity. It is not clear, however, how our knowledge could be extended to describe collective near-equilibrium motions of multidomain enzymes. We examined the effect of domain interactions on the low temperature near equilibrium dynamics of the native state, using phosphoglycerate kinase as model protein. We measured thermal activation of tryptophan phosphorescence quenching to explore millisecond-range protein motions. The two protein domains of phosphoglycerate kinase correspond to two dynamic units, but interdomain interactions link the motion of the two domains. The effect of the interdomain interactions on the activation of motions in the individual domains is asymmetric. As the temperature of the frozen protein is increased from the cryogenic, motions of the N domain are activated first. This is a partial activation, however, and the full dynamics of the domain becomes activated only after the activation of the C domain.


Assuntos
Fosfoglicerato Quinase/química , Temperatura Baixa , Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular , Fosfoglicerato Quinase/genética , Estrutura Terciária de Proteína , Leveduras/enzimologia
5.
J Phys Chem B ; 116(32): 9644-52, 2012 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-22775002

RESUMO

Application of porphyrins as photosensitizers is based on their light-triggered generation of reactive oxygen species (ROS) that may cause oxidative tissue damage and ultimately kill cells. Cellular membranes are the action grounds of many sensitizers due to their hydrophobic or amphiphilic character as well as the location of many of the targets attacked by ROS. Hence, the binding ability and location of porphyrins in liposomes as simple models of cellular membranes are of outstanding interest. Here we compare mesoporphyrin IX dimethyl ester (MPE) and its nonesterified form, mesoporphyrin IX dihydrochloride (MPCl). Monocomponent small unilamellar vesicles formed of various saturated phosphatidylcholines with incorporated mesoporphyrins were investigated. We determined the binding parameters and the inhomogeneous distribution functions (IDFs) by different fluorescence techniques. We found in general that the binding ability of MPE is considerably greater than that of MPCl. In the case of MPCl, the IDFs suggest that only one of the two binding site types identified earlier for MPE ("site II") exists; the other one ("site I") vanishes while a new one appears ("site III"). We can confirm that "site I" is located between the two lipid layers, "site II" is situated between the hydrocarbon chains, while the location of the novel "site III" is along the outer part of the hydrocarbon chains partially inserted between the lipid head groups.


Assuntos
Membrana Celular/química , Lipossomos/química , Mesoporfirinas/química , Espectrometria de Fluorescência , Sítios de Ligação , Mesoporfirinas/classificação , Modelos Moleculares , Fármacos Fotossensibilizantes/química , Protoporfirinas/química
6.
Biochim Biophys Acta ; 1820(7): 785-94, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22484033

RESUMO

BACKGROUND: The disordered Tubulin Polymerization Promoting Protein/p25 (TPPP/p25) modulates the dynamics and stability of the microtubule system. In this paper the role of dimerization in its microtubule-related functions is established, and an approach is proposed to evaluate thermodynamic constants for multiple equilibrium systems from ITC measurements. METHODS: For structural studies size exclusion chromatography, SDS-PAGE, chemical cross-linking, circular dichroism, fluorescence spectroscopy and isothermal titration calorimetry were used; the functional effect was analyzed by tubulin polymerization assay. Numerical simulation of the multiple equilibrium was performed with Mathematica software. RESULTS: The dimerization of TPPP/p25 is promoted by elevation of the protein concentration and by GTP addition. The dimeric form displaying enhanced tubulin polymerization promoting activity is stabilized by disulfide bond or chemical cross-linking. The GTP binding to the dimeric form (Kd-GTP=200 µM) is tighter with one order of magnitude than to the monomeric one leading to the enrichment of the dimers. A mathematical model elaborated for the multiple equilibrium of the TPPP/p25-GTP system was validated by fitting the GTP-dependent changes of ellipticity and fluorescence signal in the course of TPPP/p25 titrations. The evaluation of the equilibrium constants rendered it possible to determine the thermodynamic parameters of the association of different TPPP/p25 forms with GTP from ITC measurements. CONCLUSIONS/GENERAL SIGNIFICANCE: The dimerization of TPPP/p25 with favorable physiological functional potency is proposed to play significant role in the fine tuning of TPPP/p25-mediated microtubule assembly; the unfolded monomers might be involved in the formation of pathological inclusions characteristic for Parkinson's disease and other synucleinopathies.


Assuntos
Calorimetria , Guanosina Trifosfato/metabolismo , Microtúbulos/metabolismo , Modelos Teóricos , Proteínas do Tecido Nervoso/metabolismo , Proteínas Recombinantes/metabolismo , Tubulina (Proteína)/metabolismo , Cromatografia em Gel , Dicroísmo Circular , Simulação por Computador , Reagentes de Ligações Cruzadas/farmacologia , Dimerização , Humanos , Proteínas do Tecido Nervoso/genética , Multimerização Proteica , Proteínas Recombinantes/genética , Termodinâmica
7.
Biochemistry ; 50(44): 9568-78, 2011 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-21995432

RESUMO

Tubulin polymerization promoting protein/p25 (TPPP/p25) modulates the dynamics and stability of the microtubule system and plays crucial role in the myelination of oligodendrocytes. Here we showed by CD, fluorescence, and NMR spectroscopies that Zn(2+) is the first ligand that induces considerable rearrangement of the disordered TPPP/p25. Zinc finger motif (His(2)Cys(2)) (His(61)-Cys(83)) was identified within the flexible region of TPPP/p25 straddled by extended unstructured N- and C-terminal regions. The specific binding of the Zn(2+) to TPPP/p25 induced the formation of molten globule but not that of a well-defined tertiary structure. The Zn(2+)-induced partially folded structure accommodating the zinc binding motif is localized at the single Trp(76)-containing region as demonstrated by fluorescence resonance energy transfer and quenching experiments. We showed that the Zn(2+)-induced change in the TPPP/p25 structure modified its interaction with tubulin and GTP coupled with functional consequences: the TPPP/p25-promoted tubulin polymerization was increased while the TPPP/p25-catalyzed GTPase activity was decreased as detected by turbidimetry and by malachite green phosphate release/(31)P NMR assays, respectively. The finding that the Zn(2+) of the bivalent cations can uniquely influence physiological relavant interactions significantly contributes to our understanding of the role of Zn(2+)-related TPPP/p25 processes in the differentiation/myelination of oligodendrocytes possessing a high-affinity Zn(2+) uptake mechanism.


Assuntos
GTP Fosfo-Hidrolases/metabolismo , Microtúbulos/química , Proteínas do Tecido Nervoso/química , Zinco/química , Motivos de Aminoácidos , Sequência de Aminoácidos , GTP Fosfo-Hidrolases/química , Humanos , Ligantes , Microtúbulos/enzimologia , Microtúbulos/patologia , Dados de Sequência Molecular , Proteínas do Tecido Nervoso/antagonistas & inibidores , Proteínas do Tecido Nervoso/fisiologia , Polimerização , Ligação Proteica
8.
Arch Biochem Biophys ; 511(1-2): 88-100, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21549683

RESUMO

l-nucleoside analogues are now largely used as antiviral drugs for the treatment of viral infections like HBV, HCV and HIV. However, in order to be fully active, they need to be phosphorylated by cellular or viral kinases. Human 3-phosphogycerate kinase (hPGK) was shown to catalyze the last step of activation of l-enantiomers and thus constitutes an attractive target for theoretical predictions of its phosphorylation efficiency. Molecular dynamics simulations were carried out with four different nucleotides (d-/l-ADP and d-/l-CDP) in complex with hPGK and 1,3-bisphospho-d-glycerate (bPG). The binding affinities of CDPs (both enantiomers) for hPGK were found very weak while d- and l-ADP were better substrates. Interestingly, the binding affinity of the bPG substrate was found to be lower in presence of d-ADP than l-ADP which indicates a potential antagonistic effect on one substrate to the other. A detailed analysis of the simulations unravels important dynamic conditions for efficient phosphorylation. Indeed, as previously described for the natural substrate, the hinge bending motion of the domains upon substrates binding should be more correlated and directional. Interestingly, the unforeseen finding was the larger dynamics freedoms observed for the substrates that was favored by the protein atoms flexibility around the nucleobase binding site.


Assuntos
Nucleotídeos/metabolismo , Fosfoglicerato Quinase/metabolismo , Difosfato de Adenosina/química , Difosfato de Adenosina/metabolismo , Domínio Catalítico , Cistina Difosfato/química , Cistina Difosfato/metabolismo , Humanos , Cinética , Ligantes , Modelos Moleculares , Simulação de Dinâmica Molecular , Nucleotídeos/química , Fosfoglicerato Quinase/química , Conformação Proteica , Estrutura Terciária de Proteína , Eletricidade Estática , Estereoisomerismo , Especificidade por Substrato
9.
J Phys Chem B ; 115(19): 5707-15, 2011 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-21395276

RESUMO

Conformational dynamics of proteins is of fundamental importance in their physiological functions. The exact mechanisms and determinants of protein motions, including the regulatory interplay between protein and solvent motions, are not yet fully understood. In the present work, the thermal activation of phosphorescence quenching was measured in oxygen-saturated aqueous protein solutions to explore protein dynamics in the millisecond range. The sample was brought to cryogenic temperatures in a fast cooling process to avoid the bulk crystallization of ice. The phosphorescence quenching effect was followed by the phosphorescence lifetime of either Zn-protoporphyrin substituting the heme in the ß-subunits of human hemoglobin (Zn-HbA) or tryptophan residues of Zn-HbA and human myoglobin (Mb), measured in thermal equilibrium at temperatures varied from 8 to 273 K. The quenching effect was attributed primarily to the activation of collisions with O(2) molecules made possible by the activated millisecond time-scale dynamics of the matrix around the chromophores. We find that, in the studied temperature range, the activation of protein global dynamics facilitating oxygen diffusion takes place at clearly separated lower temperatures and independently from bulk solvent dynamics and that the energy and entropy differences between the studied frozen and thermally activated states are specific for the protein.


Assuntos
Simulação de Dinâmica Molecular , Mioglobina/química , Solventes/química , Corantes Fluorescentes/química , Humanos , Subunidades Proteicas/química , Protoporfirinas/química , Temperatura , Termodinâmica , Fatores de Tempo , Triptofano/química , Zinco/química
10.
FEBS Lett ; 584(6): 1139-42, 2010 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-20132817

RESUMO

Amyloid deposits, which accumulate in numerous diseases, are the final stage of multi-step protein conformational-conversion and oligomerization processes. The underlying molecular mechanisms are not fully understood, and particularly little is known about the reverse reaction. Here we show that phosphoglycerate kinase amyloid fibrils can be converted back into native protein. We achieved recovery with 60% efficiency, which is comparable to the success rate of the unfolding-refolding studies, and the recovered enzyme was folded, stable and fully active. The key intermediate stages in the recovery process are fibril disassembly and unfolding followed by spontaneous protein folding.


Assuntos
Amiloide/química , Fosfoglicerato Quinase/isolamento & purificação , Fosfoglicerato Quinase/fisiologia , Amiloide/metabolismo , Técnicas de Laboratório Clínico , Estabilidade Enzimática , Concentração de Íons de Hidrogênio , Concentração Osmolar , Fosfoglicerato Quinase/química , Fosfoglicerato Quinase/metabolismo , Desnaturação Proteica , Dobramento de Proteína , Saccharomyces cerevisiae/enzimologia , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Temperatura
11.
Biochemistry ; 48(24): 5689-99, 2009 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-19432419

RESUMO

Beta(2)-microglobulin- (beta2m-) based fibril deposition is the key symptom in dialysis-related amyloidosis. beta2m readily forms amyloid fibrils in vitro at pH 2.5. However, it is not well understood which factors promote this process in vivo, because beta2m cannot polymerize at neutral pH without additives even at elevated concentration. Here we show that lysophosphatidic acid (LPA), an in vivo occurring lysophospholipid mediator, promotes amyloid formation under physiological conditions through a complex mechanism. In the presence of LPA, at and above its critical micelle concentration, native beta2m became sensitive to limited proteolytic digestion, indicating increased conformational flexibility. Isothermal titration calorimetry indicates that beta2m exhibits high affinity for LPA. Fluorescence and CD spectroscopy, as well as calorimetry, showed that LPA destabilizes the structure of monomeric beta2m inducing a partially unfolded form. This intermediate is capable of fibril extension in a nucleation-dependent manner. Our findings also indicate that the molecular organization of fibrils formed under physiological conditions differs from that of fibrils formed at pH 2.5. Fibrils grown in the presence of LPA depolymerize very slowly in the absence of LPA; moreover, LPA stabilizes the fibrils even below its critical micelle concentration. Neither the amyloidogenic nor the fibril-stabilizing effects of LPA were mimicked by its structural and functional lysophospholipid analogues, showing its selectivity. On the basis of our findings and the observed increase in blood LPA levels in dialysis patients, we suggest that the interaction of LPA with beta2m might contribute to the pathomechanism of dialysis-related amyloidosis.


Assuntos
Amiloide/química , Lisofosfolipídeos/farmacologia , Microglobulina beta-2/química , Amiloide/metabolismo , Amiloide/ultraestrutura , Sítios de Ligação , Dicroísmo Circular , Concentração de Íons de Hidrogênio , Modelos Moleculares , Concentração Osmolar , Dobramento de Proteína , Estrutura Secundária de Proteína , Temperatura , Microglobulina beta-2/metabolismo , Microglobulina beta-2/ultraestrutura
12.
Proteins ; 77(2): 319-29, 2009 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-19422062

RESUMO

3-Phosphogycerate kinase (PGK) is a two domain enzyme, with a binding site of the 1,3-bisphosphoglycerate on the N-domain and of the ADP on the C-domain. To transfer a phosphate group the enzyme has to undergo a hinge bending motion from open to closed conformation to bring the substrates to close proximity. Molecular dynamics simulation was used to elucidate the effect of ligand binding onto the domain motions of this enzyme. The simulation results of the apo form indicate a hinge bending motion in the ns timescale while the time period of the hinge bending motion of the complex form is clearly over the 20 ns simulation time. The apo form exhibits several hinge points that contribute to the hinge bending motion while upon binding the ligands, the hinge bending becomes strictly restrained with one dominant hinge point in the vicinity of the substrates. At the same time, ligand binding results in an enhanced correlation of internal domain motions.


Assuntos
Fosfoglicerato Quinase/metabolismo , Estrutura Terciária de Proteína/fisiologia , Sítios de Ligação , Simulação por Computador , Ácidos Difosfoglicéricos/metabolismo , Humanos , Ligantes , Modelos Moleculares , Fosfoglicerato Quinase/química , Ligação Proteica , Termodinâmica
13.
J Phys Chem B ; 113(21): 7716-24, 2009 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-19408910

RESUMO

Binding of photosensitizers to target cells is a crucial step during the photodynamic effect. Sensitizer distribution is a good indication of whether the chemical is a good candidate for perturbing cell membrane integrity. Hence, the photophysical properties of porphyrinoid sensitizers in microheterogeneous systems such as liposomes are of outstanding interest. Here we present a site-selective fluorescence study of liposome systems. Monocomponent, small unilamellar vesicles formed of different phosphatidylcholines with incorporated mesoporphyrin were investigated. The size distribution of liposomes was measured by dynamic light scattering after each step of the experiment. On the basis of fluorescence line narrowing spectra of mesoporphyrin, the inhomogeneous distribution function was determined in order to characterize the photosensitizer location. The dual character of the functions revealed two different locations. Decomposition of the inhomogeneous distribution functions into Gaussians and the analysis of the fit results suggest that one of the locations for mesoporphyrin is between the two lipid layers, and the other one is between the hydrocarbon chains of the lipid molecules.


Assuntos
Lipossomos/química , Mesoporfirinas/química , Fármacos Fotossensibilizantes/química , Luz , Bicamadas Lipídicas/química , Modelos Químicos , Fotoquímica , Espalhamento de Radiação , Espectrometria de Fluorescência
14.
Biochim Biophys Acta ; 1784(12): 1965-74, 2008 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-18805513

RESUMO

The structure and activity of native horseradish peroxidase C (HRP) is stabilized by two bound Ca(2+) ions. Earlier studies suggested a critical role of one of the bound Ca(2+) ions but with conflicting conclusions concerning their respective importance. In this work we compare the native and totally Ca(2+)-depleted forms of the enzyme using pH-, pressure-, viscosity- and temperature-dependent UV absorption, CD, H/D exchange-FTIR spectroscopy and by binding the substrate benzohydroxamic acid (BHA). We report that Ca(2+)-depletion does not change the alpha helical content of the protein, but strongly modifies the tertiary structure and dynamics to yield a homogeneously loosened molten globule-like structure. We relate observed tertiary changes in the heme pocket to changes in the dipole orientation and coordination of a distal water molecule. Deprotonation of distal His42, linked to Asp43, itself coordinated to the distal Ca(2+), perturbs a H-bonding network connecting this Ca(2+) to the heme crevice that involves the distal water. The measured effects of Ca(2)(+) depletion can be interpreted as supporting a structural role for the distal Ca(2+) and for its enhanced significance in finetuning the protein structure to optimize enzyme activity.


Assuntos
Armoracia/enzimologia , Cálcio/química , Peroxidase do Rábano Silvestre/química , Proteínas de Plantas/química , Dobramento de Proteína , Dicroísmo Circular/métodos , Concentração de Íons de Hidrogênio , Estrutura Terciária de Proteína/fisiologia , Espectroscopia de Infravermelho com Transformada de Fourier/métodos
15.
J Med Chem ; 51(11): 3081-93, 2008 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-18459732

RESUMO

We report results of 12 ns, all-atom molecular dynamics simulation (MDS) and Poisson-Boltzmann free energy calculations (PBFE) on calmodulin (CaM) bound to two molecules of trifluoperazine (TFP) and of N-(3,3, diphenylpropyl)- N'-[1- R-(3,4-bis-butoxyphenyl)-ethyl]-propylenediamine (DPD). X-ray data show very similar structures for the two complexes, yet the antagonists significantly differ with respect to their CaM binding affinities, the neutral DPD is much more potent. The goal of the study was to unravel the reason why TFP is less potent although its positive charge should facilitate binding. The electrostatic energy terms in CHARMM and binding free energy terms of the PBFE approach showed TFP a better antagonist, while inspection of hydrophobic contacts supports DPD binding. Detailed inspection of the amino acid contributions of PBFE calculations unravel that steric reasons oppose the favorable binding of TFP. Structural conditions are given for a successful drug design strategy, which may benefit also from charge-charge interactions.


Assuntos
Calmodulina/antagonistas & inibidores , Calmodulina/química , Fendilina/análogos & derivados , Modelos Moleculares , Trifluoperazina/química , Sítios de Ligação , Simulação por Computador , Fendilina/química , Interações Hidrofóbicas e Hidrofílicas , Estrutura Molecular , Ligação Proteica , Eletricidade Estática , Termodinâmica
16.
Proteins ; 71(1): 308-19, 2008 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-17932923

RESUMO

dUTP pyrophosphatase, a preventive DNA repair enzyme, contributes to maintain the appropriate cellular dUTP/dTTP ratio by catalyzing dUTP hydrolysis. dUTPase is essential for viability in bacteria and eukaryotes alike. Identification of species-specific antagonists of bacterial dUTPases is expected to contribute to the development of novel antimicrobial agents. As a first general step, design of dUTPase inhibitors should be based on modifications of the substrate dUTP phosphate chain, as modifications in either base or sugar moieties strongly impair ligand binding. Based on structural differences between bacterial and human dUTPases, derivatization of dUTP-analogous compounds will be required as a second step to invoke species-specific character. Studies performed with dUTP analogues also offer insights into substrate binding characteristics of this important and structurally peculiar enzyme. In this study, alpha,beta-methylene-dUDP was synthesized and its complex with dUTPase was characterized. Enzymatic phosphorylation of this substrate analogue by pyruvate kinase was not possible in contrast to the successful enzymatic phosphorylation of alpha,beta-imino-dUDP. One explanation for this finding is that the different bond angles and the presence of the methylene group may preclude formation of a catalytically competent complex with the kinase. Crystal structure of E. coli dUTPase:alpha,beta-methylene-dUDP and E. coli dUTPase:dUDP:Mn complexes were determined and analyzed in comparison with previous data. Results show that the "trans" alpha-phosphate conformation of alpha,beta-methylene-dUDP differs from the catalytically competent "gauche" alpha-phosphate conformation of the imino analogue and the oxo substrate, manifested in the shifted position of the alpha-phosphorus by more than 3 A. The three-dimensional structures determined in this work show that the binding of the methylene analogue with the alpha-phosphorus in the "gauche" conformation would result in steric clash of the methylene group with the protein atoms. In addition, the metal ion cofactor was not bound in the crystal of the complex with the methylene analogue while it was clearly visible as coordinated to dUDP, arguing that the altered phosphate chain conformation also perturbs metal ion complexation. Isothermal calorimetry titrations indicate that the binding affinity of alpha,beta-methylene-dUDP toward dUTPase is drastically decreased when compared with that of dUDP. In conclusion, the present data suggest that while alpha,beta-methylene-dUDP seems to be practically nonhydrolyzable, it is not a strong binding inhibitor of dUTPase probably due to the altered binding mode of the phosphate chain. Results indicate that in some cases methylene analogues may not faithfully reflect the competent substrate ligand properties, especially if the methylene hydrogens are in steric conflict with the protein.


Assuntos
Proteínas de Escherichia coli/química , Pirofosfatases/química , Difosfato de Uridina/análogos & derivados , Sítios de Ligação , Ligantes , Ligação Proteica , Especificidade por Substrato , Difosfato de Uridina/química
17.
FEBS Lett ; 581(24): 4783-8, 2007 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-17880943

RESUMO

Human dUTPase, essential for DNA integrity, is an important survival factor for cancer cells. We determined the crystal structure of the enzyme:alpha,beta-imino-dUTP:Mg complex and performed equilibrium binding experiments in solution. Ordering of the C-terminus upon the active site induces close juxtaposition of the incoming nucleophile attacker water oxygen and the alpha-phosphorus of the substrate, decreasing their distance below the van der Waals limit. Complex interactions of the C-terminus with both substrate and product were observed via a specifically designed tryptophan sensor, suitable for further detailed kinetic and ligand binding studies. Results explain the key functional role of the C-terminus.


Assuntos
Pirofosfatases/química , Pirofosfatases/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Catálise , Cristalografia por Raios X , Humanos , Ligantes , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Subunidades Proteicas/química , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Pirofosfatases/genética
18.
Biochim Biophys Acta ; 1768(6): 1650-8, 2007 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-17459331

RESUMO

The activation energy and activation volume of the spectral blue shift subsequent to protochlorophyllide phototransformation (called Shibata shift in intact leaves) were studied in prolamellar body (PLB) and prothylakoid-(PT)-enriched membrane fractions prepared from dark-grown wheat (Triticum aestivum, L.) leaves. The measurements were done at 20, 30 and 40 degrees C and at various pressure values. The activation energy values were 181+/-8 kJ mol(-1) and 188+/-6 kJ mol(-1) for the PLBs and the PTs, respectively. The pressure stabilized the structure of the NADPH:protochlorophyllide oxidoreductase (POR) macrodomains; it prevented or slowed down the blue shift. There were no significant differences between the activation volumes of PLBs and PTs at 30 or 40 degrees C giving values around 100-125 ml mol(-1) which correspond to changes in the tertiary structure of proteins but also resemble the volume changes occurring during the disaggregation of protein dimers or oligomers, or during dissociation of peripheral membrane proteins from membranes. The small differences in the activation parameters of PLBs and PTs indicate that molecular rearrangements inside the POR macrodomains are the primary reasons of the fluorescence blue shift; however, their lipid microenvironment must be also important in the initialization of the shift.


Assuntos
Oxirredutases atuantes sobre Doadores de Grupo CH-CH/química , Folhas de Planta/química , Protoclorifilida/química , Tilacoides/química , Triticum/química , Fluorescência , Cinética , Fotoquímica , Pressão , Estrutura Terciária de Proteína , Análise Espectral , Temperatura
19.
Biophys J ; 92(5): 1709-16, 2007 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-17158564

RESUMO

A 3-ns molecular dynamics simulation in explicit solvent was performed to examine the inter- and intradomain motions of the two-domain enzyme yeast phosphoglycerate kinase without the presence of substrates. To elucidate contributions from individual domains, simulations were carried out on the complete enzyme as well as on each isolated domain. The enzyme is known to undergo a hinge-bending type of motion as it cycles from an open to a closed conformation to allow the phosphoryl transfer occur. Analysis of the correlation of atomic movements during the simulations confirms hinge bending in the nanosecond timescale: the two domains of the complete enzyme exhibit rigid body motions anticorrelated with respect to each other. The correlation of the intradomain motions of both domains converges, yielding a distinct correlation map in the enzyme. In the isolated domain simulations-in which interdomain interactions cannot occur-the correlation of domain motions no longer converges and shows a very small correlation during the same simulation time. This result points to the importance of interdomain contacts in the overall dynamics of the protein. The secondary structure elements responsible for interdomain contacts are also discussed.


Assuntos
Simulação por Computador , Proteínas Fúngicas/química , Modelos Moleculares , Movimento (Física) , Fosfoglicerato Quinase/química , Estrutura Secundária de Proteína
20.
J Biol Chem ; 281(36): 25972-83, 2006 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-16822864

RESUMO

The contribution of heterotropic effectors to hemoglobin allostery is still not completely understood. With the recently proposed global allostery model, this question acquires crucial significance, because it relates tertiary conformational changes to effector binding in both the R- and T-states. In this context, an important question is how far the induced conformational changes propagate from the binding site(s) of the allosteric effectors. We present a study in which we monitored the interdimeric interface when the effectors such as Cl-, 2,3-diphosphoglycerate, inositol hexaphosphate, and bezafibrate were bound. We studied oxy-Hb and a hybrid form (alphaFeO2)2-(betaZn)2 as the T-state analogue by monitoring heme absorption and Trp intrinsic fluorescence under hydrostatic pressure. We observed a pressure-dependent change in the intrinsic fluorescence, which we attribute to a pressure-induced tetramer to dimer transition with characteristic pressures in the 70-200-megapascal range. The transition is sensitive to the binding of allosteric effectors. We fitted the data with a simple model for the tetramer-dimer transition and determined the dissociation constants at atmospheric pressure. In the R-state, we observed a stabilizing effect by the allosteric effectors, although in the T-analogue a stronger destabilizing effect was seen. The order of efficiency was the same in both states, but with the opposite trend as inositol hexaphosphate > 2,3-diphosphoglycerate > Cl-. We detected intrinsic fluorescence from bound bezafibrate that introduced uncertainty in the comparison with other effectors. The results support the global allostery model by showing that conformational changes propagate from the effector binding site to the interdimeric interfaces in both quaternary states.


Assuntos
2,3-Difosfoglicerato/metabolismo , Bezafibrato/metabolismo , Cloretos/metabolismo , Hemoglobina A , Hipolipemiantes/metabolismo , Ácido Fítico/metabolismo , Estrutura Quaternária de Proteína , 2,3-Difosfoglicerato/química , Regulação Alostérica , Animais , Bezafibrato/química , Sítios de Ligação , Cloretos/química , Dimerização , Hemoglobina A/química , Hemoglobina A/metabolismo , Cavalos , Humanos , Hipolipemiantes/química , Modelos Moleculares , Mioglobina/química , Mioglobina/metabolismo , Oxirredução , Ácido Fítico/química , Porfirinas/química , Ligação Proteica , Espectrometria de Fluorescência , Triptofano/química
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