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1.
Biochemistry ; 57(28): 4063-4073, 2018 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-29894640

RESUMO

Phospholipids and sterols play multiple roles in cells. In addition to establishing barriers between compartments, they also provide the matrix for assembly and function of a large variety of catalytic processes. Lipid composition is a highly regulated feature of biological membranes, yet its implications for membrane proteins are difficult problems to approach. One obstacle is the inherent complexity of observing and describing these interactions and their dynamics at a molecular and atomic level. However, lipid interactions are pivotal for membrane protein function and should be acknowledged. The enzymatic activity of several different P-type ATPases, one of the major families of ion pumping primary active transporters, has previously been shown to exhibit a strong dependence on phospholipids; however, distinguishing the effects of annular and specific lipid interactions is challenging. Here we show that the hydrolytic activity of a bacterial Cu(I)-transporting P-type ATPase (LpCopA) is stimulated by the bacterial, anionic phospholipid cardiolipin and to some extent by phosphatidylglycerol. Furthermore, multiscale molecular dynamics simulations pinpoint lipid hot spots on the membrane-spanning domain of LpCopA. Thus, using two independent methods, our study shows converging evidence that the lipid membrane composition plays an important role for LpCopA.


Assuntos
Proteínas de Bactérias/metabolismo , Cardiolipinas/metabolismo , ATPases Transportadoras de Cobre/metabolismo , Legionella pneumophila/enzimologia , Fosfatidilgliceróis/metabolismo , Proteínas de Bactérias/química , ATPases Transportadoras de Cobre/química , Humanos , Hidrólise , Legionella pneumophila/química , Legionella pneumophila/metabolismo , Doença dos Legionários/microbiologia , Lipídeos de Membrana/metabolismo , Simulação de Dinâmica Molecular , Domínios Proteicos
2.
J Biol Chem ; 291(33): 16963-76, 2016 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-27339893

RESUMO

The complement system is an important part of the innate immune response to infection but may also cause severe complications during inflammation. Small molecule antagonists to complement receptor 3 (CR3) have been widely sought, but a structural basis for their mode of action is not available. We report here on the structure of the human CR3 ligand-binding I domain in complex with simvastatin. Simvastatin targets the metal ion-dependent adhesion site of the open, ligand-binding conformation of the CR3 I domain by direct contact with the chelated Mg(2+) ion. Simvastatin antagonizes I domain binding to the complement fragments iC3b and C3d but not to intercellular adhesion molecule-1. By virtue of the I domain's wide distribution in binding kinetics to ligands, it was possible to identify ligand binding kinetics as discriminator for simvastatin antagonism. In static cellular experiments, 15-25 µm simvastatin reduced adhesion by K562 cells expressing recombinant CR3 and by primary human monocytes, with an endogenous expression of this receptor. Application of force to adhering monocytes potentiated the effects of simvastatin where only a 50-100 nm concentration of the drug reduced the adhesion by 20-40% compared with untreated cells. The ability of simvastatin to target CR3 in its ligand binding-activated conformation is a novel mechanism to explain the known anti-inflammatory effects of this compound, in particular because this CR3 conformation is found in pro-inflammatory environments. Our report points to new designs of CR3 antagonists and opens new perspectives and identifies druggable receptors from characterization of the ligand binding kinetics in the presence of antagonists.


Assuntos
Antígeno de Macrófago 1 , Monócitos/metabolismo , Sinvastatina , Complemento C3b/química , Complemento C3b/metabolismo , Humanos , Células K562 , Antígeno de Macrófago 1/química , Antígeno de Macrófago 1/metabolismo , Magnésio/química , Magnésio/metabolismo , Domínios Proteicos , Sinvastatina/química , Sinvastatina/farmacologia
3.
J Neurochem ; 142(1): 171-182, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-28407243

RESUMO

Prion diseases are associated with the misfolding of the prion protein (PrP) from its normal cellular form (PrPC ) to its infectious scrapie form (PrPSc ). Post-translational modifications in PrP in vivo can play an important role in modulating the process of misfolding. To gain more insight into the effects of post-translational modifications in PrP structure and dynamics and to test the hypothesis that such modifications can interact with the protein, we have performed molecular dynamics simulations of diglycosylated human PrPC bound to a lipid bilayer via a glycophosphatidylinositol anchor. Multiple simulations were performed at three different pH ranges to explore pH effects on structure and dynamics. In contrast to simulations of protein-only PrPC , no large effects were observed upon lowering the pH of the system. The protein tilted toward the membrane surface in all of the simulations and the putative PrPSc oligomerization sites became inaccessible, thereby offering a possible protective mechanism against PrPSc -induced misfolding of PrPC .


Assuntos
Proteínas Priônicas/química , Deficiências na Proteostase , Simulação por Computador , Glicosilação , Humanos , Bicamadas Lipídicas , Membranas/metabolismo , Modelos Moleculares , Simulação de Acoplamento Molecular , Fosfatidilinositóis/química , Conformação Proteica , Processamento de Proteína Pós-Traducional
4.
Biochim Biophys Acta Biomembr ; 1859(3): 340-349, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27993564

RESUMO

Lipases are enzymes of biotechnological importance that function at the interface formed between hydrophobic and aqueous environments. Hydrophobic interfaces can induce structural transitions in lipases that result in an increase in enzyme activity, although the detailed mechanism of this process is currently not well understood for many lipases. Here, we present a multi-scale molecular dynamics simulation study of how different interfaces affect the conformational dynamics of the psychrophilic lipase M37. Our simulations show that M37 lipase is able to interact both with anionic lipid bilayers and with triglyceride surfaces. Interfacial interactions with triglyceride surfaces promote large-scale motions of the lid region of M37, spanning residues 235-283, revealing an entry pathway to the catalytic site for substrates. Importantly, these results suggest a potential activation mechanism for M37 that deviates from other related enzymes, such as Thermomyces lanuginosus lipase. We also investigated substrate binding in M37 by using steered MD simulations, confirming the open state of this lipase. The exposure of hydrophobic residues within lid and active site flap regions (residues 94-110) during the activation process provides insights into the functional effect of hydrophobic surfaces on lipase activation.


Assuntos
Proteínas de Bactérias/metabolismo , Lipase/metabolismo , Proteínas de Bactérias/química , Domínio Catalítico , Lipase/química , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Simulação de Dinâmica Molecular , Photobacterium/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína , Especificidade por Substrato , Água/química , Água/metabolismo
5.
Biochemistry ; 55(45): 6238-6249, 2016 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-27786441

RESUMO

The exchange of ADP and ATP across the inner mitochondrial membrane is a fundamental cellular process. This exchange is facilitated by the adenine nucleotide translocase, the structure and function of which are critically dependent on the signature phospholipid of mitochondria, cardiolipin (CL). Here we employ multiscale molecular dynamics simulations to investigate CL interactions within a membrane environment. Using simulations at both coarse-grained and atomistic resolutions, we identify three CL binding sites on the translocase, in agreement with those seen in crystal structures and inferred from nuclear magnetic resonance measurements. Characterization of the free energy landscape for lateral lipid interaction via potential of mean force calculations demonstrates the strength of interaction compared to those of binding sites on other mitochondrial membrane proteins, as well as their selectivity for CL over other phospholipids. Extending the analysis to other members of the family, yeast Aac2p and mouse uncoupling protein 2, suggests a degree of conservation. Simulation of large patches of a model mitochondrial membrane containing multiple copies of the translocase shows that CL interactions persist in the presence of protein-protein interactions and suggests CL may mediate interactions between translocases. This study provides a key example of how computational microscopy may be used to shed light on regulatory lipid-protein interactions.


Assuntos
Translocador 1 do Nucleotídeo Adenina/metabolismo , Cardiolipinas/metabolismo , Membranas Mitocondriais/metabolismo , Simulação de Dinâmica Molecular , Translocador 1 do Nucleotídeo Adenina/química , Animais , Sítios de Ligação , Cardiolipinas/química , Bovinos , Cristalografia por Raios X , Espectroscopia de Ressonância Magnética , Camundongos , Translocases Mitocondriais de ADP e ATP/química , Translocases Mitocondriais de ADP e ATP/metabolismo , Ligação Proteica , Domínios Proteicos , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Termodinâmica , Proteína Desacopladora 2/química , Proteína Desacopladora 2/metabolismo
6.
Biochim Biophys Acta ; 1850(5): 1017-1025, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25219456

RESUMO

BACKGROUND: The epidermal growth factor receptor (EGFR) is the best characterised member of the receptor tyrosine kinases, which play an important role in signalling across mammalian cell membranes. The EGFR juxtamembrane (JM) domain is involved in the mechanism of activation of the receptor, interacting with the anionic lipid phosphatidylinositol 4,5-bisphosphate (PIP2) in the intracellular leaflet of the cell membrane. METHODS: Multiscale MD simulations were used to characterize PIP2-JM interactions. Simulations of the transmembrane helix plus JM region (TM-JM) dimer (PDB:2M20) in both PIP2-containing and PIP2-depleted lipid bilayer membranes revealed the interactions of the JM with PIP2 and other lipids. RESULTS: PIP2 forms strong interactions with the basic residues in the R645-R647 motif of the JM domain resulting in clustering of PIP2 around the protein. This association of PIP2 and the JM domain aids stabilization of JM-A dimer away from the membrane. Mutation (R645N/R646N/R647N) or PIP2-depletion results in deformation of the JM-A dimer and changes in JM-membrane interactions. CONCLUSIONS: These simulations support the proposal that the positively charged residues at the start of the JM-A domain stabilize the JM-A helices in an orientation away from the membrane surface through binding to PIP2, thus promoting a conformation corresponding to an asymmetric (i.e. activated) kinase. GENERAL SIGNIFICANCE: This study indicates that MD simulations may be used to characterise JM/lipid interactions, thus helping to define their role in the mechanisms of receptor tyrosine kinases. This article is part of a Special Issue entitled Recent developments of molecular dynamics.


Assuntos
Receptores ErbB/química , Bicamadas Lipídicas/química , Simulação de Dinâmica Molecular , Fosfatidilinositol 4,5-Difosfato/química , Ativação Enzimática , Estabilidade Enzimática , Receptores ErbB/genética , Receptores ErbB/metabolismo , Bicamadas Lipídicas/metabolismo , Mutação , Fosfatidilinositol 4,5-Difosfato/metabolismo , Ligação Proteica , Multimerização Proteica , Estrutura Terciária de Proteína , Relação Estrutura-Atividade
7.
Soft Matter ; 12(37): 7792-7803, 2016 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-27722554

RESUMO

The ease with which a cell membrane can bend and deform is important for a wide range of biological functions. Peripheral proteins that induce curvature in membranes (e.g. BAR domains) have been studied for a number of years. Little is known, however, about the effect of integral membrane proteins on the stiffness of a membrane (characterised by the bending rigidity, Kc). We demonstrate by computer simulation that adding integral membrane proteins at physiological densities alters the stiffness of the membrane. First we establish that the coarse-grained MARTINI forcefield is able to accurately reproduce the bending rigidity of a small patch of 1500 phosphatidyl choline lipids by comparing the calculated value to both experiment and an atomistic simulation of the same system. This enables us to simulate the dynamics of large (ca. 50 000 lipids) patches of membrane using the MARTINI coarse-grained description. We find that altering the lipid composition changes the bending rigidity. Adding integral membrane proteins to lipid bilayers also changes the bending rigidity, whilst adding a simple peripheral membrane protein has no effect. Our results suggest that integral membrane proteins can have different effects, and in the case of the bacterial outer membrane protein, BtuB, the greater the density of protein, the larger the reduction in stiffness.


Assuntos
Membrana Celular/química , Proteínas de Membrana/química , Fosfatidilcolinas/química , Simulação por Computador , Bicamadas Lipídicas/química , Simulação de Dinâmica Molecular
8.
Bioorg Med Chem ; 24(12): 2725-38, 2016 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-27160055

RESUMO

The human serotonin transporter is the primary target of several antidepressant drugs, and the importance of a primary, high affinity binding site (S1) for antidepressant binding is well documented. The existence of a lower affinity, secondary binding site (S2) has, however, been debated. Herein we report the synthesis of 3-position coupled imipramine ligands from clomipramine using a copper free Sonogashira reaction. Ligand design was inspired by results from docking and steered molecular dynamics simulations, and the ligands were utilized in a structure-activity relationship study of the positional relationship between the S1 and S2 sites. The computer simulations suggested that the S2 site does indeed exist although with lower affinity for imipramine than observed within the S1 site. Additionally, it was possible to dock the 3-linked imipramine analogs into positions which occupy the S1 and the S2 site simultaneously. The structure activity relationship study showed that the shortest ligands were the most potent, and mutations enlarging the proposed S2 site were found to affect the larger ligands positively, while the smaller ligands were mostly unaffected.


Assuntos
Antidepressivos/química , Antidepressivos/farmacologia , Imipramina/análogos & derivados , Imipramina/farmacologia , Inibidores Seletivos de Recaptação de Serotonina/química , Inibidores Seletivos de Recaptação de Serotonina/farmacologia , Proteínas da Membrana Plasmática de Transporte de Serotonina/metabolismo , Antidepressivos/síntese química , Humanos , Imipramina/síntese química , Simulação de Acoplamento Molecular , Mutação , Serotonina/metabolismo , Proteínas da Membrana Plasmática de Transporte de Serotonina/química , Proteínas da Membrana Plasmática de Transporte de Serotonina/genética , Inibidores Seletivos de Recaptação de Serotonina/síntese química , Relação Estrutura-Atividade
9.
Biophys J ; 108(6): 1390-1399, 2015 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-25809252

RESUMO

The leucine transporter (LeuT) is a bacterial homolog of the human monoamine transporters, which are important pharmaceutical targets. There are no high-resolution structures of the human transporters available; however, LeuT has been crystallized in several different conformational states. Recently, an inward-facing conformation of LeuT was solved revealing an unexpectedly large movement of transmembrane helix 1a (TM1a). We have performed molecular dynamics simulations of the mutated and wild-type transporter, with and without the cocrystallized Fab antibody fragment, to investigate the properties of this inward-facing conformation in relation to transport by LeuT within the membrane environment. In all of the simulations, local conformational changes with respect to the crystal structure are consistently observed, especially in TM1a. Umbrella sampling revealed a soft potential for TM1a tilting. Furthermore, simulations of inward-facing LeuT with Na(+) ions and substrate bound suggest that one of the Na(+) ion binding sites is fully disrupted. Release of alanine and the second Na(+) ion is also observed, giving insight into the final stage of the translocation process in atomistic detail.


Assuntos
Sistemas de Transporte de Aminoácidos/química , Proteínas de Bactérias/química , Proteínas da Membrana Plasmática de Transporte de Neurotransmissores/química , Alanina/química , Proteínas de Bactérias/genética , Sítios de Ligação , Íons/química , Simulação de Dinâmica Molecular , Mutação , Proteínas da Membrana Plasmática de Transporte de Neurotransmissores/genética , Conformação Proteica , Estabilidade Proteica , Sódio/química
10.
Biochemistry ; 54(36): 5546-56, 2015 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-26305369

RESUMO

The human transforming growth factor ß-induced protein (TGFBIp) is involved in several types of corneal dystrophies where protein aggregation and amyloid fibril formation severely impair vision. Most disease-causing mutations are located in the last of four homologous fasciclin-1 (FAS1) domains of the protein, and it has been shown that when isolated, the fourth FAS1 domain (FAS1-4) mimics the behavior of full-length TGFBIp. In this study, we use molecular dynamics simulations and principal component analysis to study the wild-type FAS1-4 domain along with three disease-causing mutations (R555W, R555Q, and A546T) to decipher any internal difference in dynamical properties of the domains that may explain their varied stabilities and aggregation properties. In addition, we use a protein-protein docking method in combination with chemical cross-linking experiments and mass spectrometry of the cross-linked species to obtain information about interaction faces between identical FAS1-4 domains. The results show that the pathogenic mutations A546T and R555W affect the packing in the hydrophobic core of FAS1-4 in different directions. We further show that the FAS1-4 monomers associate using their ß-rich regions, consistent with peptides observed to be part of the amyloid fibril core in lattice corneal dystrophy patients.


Assuntos
Amiloide/química , Distrofias Hereditárias da Córnea/genética , Proteínas da Matriz Extracelular/química , Fator de Crescimento Transformador beta/química , Amiloide/genética , Cromatografia Líquida , Simulação por Computador , Reagentes de Ligações Cruzadas/química , Proteínas da Matriz Extracelular/genética , Interações Hidrofóbicas e Hidrofílicas , Simulação de Dinâmica Molecular , Mutação , Succinimidas/química , Espectrometria de Massas em Tandem , Fator de Crescimento Transformador beta/genética
11.
J Am Chem Soc ; 137(46): 14694-704, 2015 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-26517394

RESUMO

The interactions of membrane proteins are influenced by their lipid environment, with key lipid species able to regulate membrane protein function. Advances in high-resolution microscopy can reveal the organization and dynamics of proteins and lipids within living cells at resolutions <200 nm. Parallel advances in molecular simulations provide near-atomic-resolution models of the dynamics of the organization of membranes of in vivo-like complexity. We explore the dynamics of proteins and lipids in crowded and complex plasma membrane models, thereby closing the gap in length and complexity between computations and experiments. Our simulations provide insights into the mutual interplay between lipids and proteins in determining mesoscale (20-100 nm) fluctuations of the bilayer, and in enabling oligomerization and clustering of membrane proteins.


Assuntos
Proteínas de Membrana/metabolismo , Proteínas de Membrana/fisiologia , Simulação de Dinâmica Molecular , Ligação Proteica
12.
PLoS Comput Biol ; 10(10): e1003911, 2014 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-25340788

RESUMO

Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.


Assuntos
Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Microdomínios da Membrana/química , Microdomínios da Membrana/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Sequência de Aminoácidos , Biologia Computacional , Simulação de Dinâmica Molecular , Dados de Sequência Molecular
13.
Mol Pharmacol ; 85(5): 703-14, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24516100

RESUMO

Inhibitors of the serotonin transporter (SERT) are widely used antidepressant agents, but the structural mechanism for inhibitory activity and selectivity over the closely related norepinephrine transporter (NET) is not well understood. Here we use a combination of chemical, biological, and computational methods to decipher the molecular basis for high-affinity recognition in SERT and selectivity over NET for the prototypical antidepressant drug fluoxetine (Prozac; Eli Lilly, Indianapolis, IN). We show that fluoxetine binds within the central substrate site of human SERT, in agreement with recent X-ray crystal structures of LeuBAT, an engineered monoamine-like version of the bacterial amino acid transporter LeuT. However, the binding orientation of fluoxetine is reversed in our experimentally supported model compared with the LeuBAT structures, emphasizing the need for careful experimental verification when extrapolating findings from crystal structures of bacterial transporters to human relatives. We find that the selectivity of fluoxetine and nisoxetine, a NET selective structural congener of fluoxetine, is controlled by residues in different regions of the transporters, indicating a complex mechanism for selective recognition of structurally similar compounds in SERT and NET. Our findings add important new information on the molecular basis for SERT/NET selectivity of antidepressants, and provide the first assessment of the potential of LeuBAT as a model system for antidepressant binding in human transporters, which is essential for future structure-based drug development of antidepressant drugs with fine-tuned transporter selectivity.


Assuntos
Antidepressivos de Segunda Geração/química , Antidepressivos de Segunda Geração/metabolismo , Fluoxetina/química , Fluoxetina/metabolismo , Inibidores Seletivos de Recaptação de Serotonina/química , Inibidores Seletivos de Recaptação de Serotonina/metabolismo , Animais , Células COS , Chlorocebus aethiops , Cristalografia por Raios X , Humanos , Proteínas da Membrana Plasmática de Transporte de Norepinefrina/antagonistas & inibidores , Proteínas da Membrana Plasmática de Transporte de Norepinefrina/metabolismo , Ligação Proteica/fisiologia , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas da Membrana Plasmática de Transporte de Serotonina/metabolismo
14.
Mol Pharmacol ; 85(2): 208-17, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24214825

RESUMO

Mazindol has been explored as a possible agent in cocaine addiction pharmacotherapy. The tetracyclic compound inhibits both the dopamine transporter and the serotonin transporter, and simple chemical modifications considerably alter target selectivity. Mazindol, therefore, is an attractive scaffold for both understanding the molecular determinants of serotonin/dopamine transporter selectivity and for the development of novel drug abuse treatments. Using molecular modeling and pharmacologic profiling of rationally chosen serotonin and dopamine transporter mutants with respect to a series of mazindol analogs has allowed us to determine the orientation of mazindol within the central binding site. We find that mazindol binds in the central substrate binding site, and that the transporter selectivity can be modulated through mutations of a few residues in the binding pocket. Mazindol is most likely to bind as the R-enantiomer. Tyrosines 95 and 175 in the human serotonin transporter and the corresponding phenylalanines 75 and 155 in the human dopamine transporter are the primary determinants of mazindol selectivity. Manipulating the interaction of substituents on the 7-position with the human serotonin transporter Tyr175 versus dopamine transporter Phe155 is found to be a strong tool in tuning the selectivity of mazindol analogs and may be used in future drug design of cocaine abuse pharmacotherapies.


Assuntos
Proteínas da Membrana Plasmática de Transporte de Dopamina/metabolismo , Mazindol/metabolismo , Proteínas da Membrana Plasmática de Transporte de Serotonina/metabolismo , Sítios de Ligação , Células Cultivadas , Transtornos Relacionados ao Uso de Cocaína/tratamento farmacológico , Humanos , Mazindol/química , Mazindol/uso terapêutico , Modelos Moleculares , Relação Estrutura-Atividade
15.
Biochim Biophys Acta ; 1834(12): 2812-22, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24129074

RESUMO

Hereditary mutations in the transforming growth factor beta induced (TGFBI) gene cause phenotypically distinct corneal dystrophies characterized by protein deposition in cornea. We show here that the Arg555Trp mutant of the fourth fasciclin 1 (FAS1-4) domain of the protein (TGFBIp/keratoepithelin/ßig-h3), associated with granular corneal dystrophy type 1, is significantly less susceptible to proteolysis by thermolysin and trypsin than the WT domain. High-resolution liquid-state NMR of the WT and Arg555Trp mutant FAS1-4 domains revealed very similar structures except for the region around position 555. The Arg555Trp substitution causes Trp555 to be buried in an otherwise empty hydrophobic cavity of the FAS1-4 domain. The first thermolysin cleavage in the core of the FAS1-4 domain occurs on the N-terminal side of Leu558 adjacent to the Arg555 mutation. MD simulations indicated that the C-terminal end of helix α3' containing this cleavage site is less flexible in the mutant domain, explaining the observed proteolytic resistance. This structural change also alters the electrostatic properties, which may explain increased propensity of the mutant to aggregate in vitro with 2,2,2-trifluoroethanol. Based on our results we propose that the Arg555Trp mutation disrupts the normal degradation/turnover of corneal TGFBIp, leading to accumulation and increased propensity to aggregate through electrostatic interactions.


Assuntos
Substituição de Aminoácidos , Distrofias Hereditárias da Córnea , Proteínas da Matriz Extracelular/química , Mutação de Sentido Incorreto , Proteólise , Fator de Crescimento Transformador beta/química , Proteínas da Matriz Extracelular/genética , Proteínas da Matriz Extracelular/metabolismo , Humanos , Estabilidade Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Fator de Crescimento Transformador beta/genética , Fator de Crescimento Transformador beta/metabolismo
16.
BMC Med Genet ; 14: 111, 2013 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-24156255

RESUMO

BACKGROUND: Imerslund-Gräsbeck Syndrome (IGS) is a rare genetic disorder characterised by juvenile megaloblastic anaemia. IGS is caused by mutations in either of the genes encoding the intestinal intrinsic factor-vitamin B12 receptor complex, cubam. The cubam receptor proteins cubilin and amnionless are both expressed in the small intestine as well as the proximal tubules of the kidney and exhibit an interdependent relationship for post-translational processing and trafficking. In the proximal tubules cubilin is involved in the reabsorption of several filtered plasma proteins including vitamin carriers and lipoproteins. Consistent with this, low-molecular-weight proteinuria has been observed in most patients with IGS. The aim of this study was to characterise novel disease-causing mutations and correlate novel and previously reported mutations with the presence of low-molecular-weight proteinuria. METHODS: Genetic screening was performed by direct sequencing of the CUBN and AMN genes and novel identified mutations were characterised by in silico and/or in vitro investigations. Urinary protein excretion was analysed by immunoblotting and high-resolution gel electrophoresis of collected urines from patients and healthy controls to determine renal phenotype. RESULTS: Genetic characterisation of nine IGS patients identified two novel AMN frameshift mutations alongside a frequently reported AMN splice site mutation and two CUBN missense mutations; one novel and one previously reported in Finnish patients. The novel AMN mutations were predicted to result in functionally null AMN alleles with no cell-surface expression of cubilin. Also, the novel CUBN missense mutation was predicted to affect structural integrity of the IF-B12 binding site of cubilin and hereby most likely cubilin cell-surface expression. Analysis of urinary protein excretion in the patients and 20 healthy controls revealed increased urinary excretion of cubilin ligands including apolipoprotein A-I, transferrin, vitamin D-binding protein, and albumin. This was, however, only observed in patients where plasma membrane expression of cubilin was predicted to be perturbed. CONCLUSIONS: In the present study, mutational characterisation of nine IGS patients coupled with analyses of urinary protein excretion provide additional evidence for a correlation between mutation type and presence of the characteristic low-molecular-weight proteinuria.


Assuntos
Túbulos Renais Proximais/fisiopatologia , Síndromes de Malabsorção/genética , Síndromes de Malabsorção/fisiopatologia , Proteínas/genética , Proteinúria/genética , Proteinúria/fisiopatologia , Receptores de Superfície Celular/genética , Deficiência de Vitamina B 12/genética , Deficiência de Vitamina B 12/fisiopatologia , Albuminúria/diagnóstico , Anemia Megaloblástica , Animais , Apolipoproteína A-I/urina , Sítios de Ligação , Células CHO , Estudos de Casos e Controles , Cricetulus , Feminino , Mutação da Fase de Leitura , Humanos , Túbulos Renais Proximais/metabolismo , Masculino , Proteínas de Membrana , Peso Molecular , Mutação de Sentido Incorreto , Linhagem , Conformação Proteica , Proteínas/metabolismo , Proteinúria/diagnóstico , Receptores de Superfície Celular/química , Receptores de Superfície Celular/metabolismo , Transferrina/urina , Proteína de Ligação a Vitamina D/urina
17.
Structure ; 31(12): 1556-1566.e3, 2023 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-37729917

RESUMO

The cation channel TRPA1 is a potentially important drug target, and characterization of TRPA1 functional dynamics might help guide structure-based drug design. Here, we present results from long-timescale molecular dynamics simulations of TRPA1 with an allosteric activator, allyl isothiocyanate (AITC), in which we observed spontaneous transitions from a closed, non-conducting channel conformation into an open, conducting conformation. Based on these transitions, we propose a gating mechanism in which movement of a regulatory TRP-like domain allosterically translates into pore opening in a manner reminiscent of pore opening in voltage-gated ion channels. In subsequent experiments, we found that mutations that disrupt packing of the S4-S5 linker-TRP-like domain and the S5 and S6 helices also affected channel activity. In simulations, we also observed A-967079, a known allosteric inhibitor, binding between helices S5 and S6, suggesting that A-967079 may suppress activity by stabilizing a non-conducting pore conformation-a finding consistent with our proposed gating mechanism.


Assuntos
Oximas , Mutação , Estrutura Secundária de Proteína
18.
PLoS Comput Biol ; 7(10): e1002246, 2011 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22046120

RESUMO

Monoamine transporters are responsible for termination of synaptic signaling and are involved in depression, control of appetite, and anxiety amongst other neurological processes. Despite extensive efforts, the structures of the monoamine transporters and the transport mechanism of ions and substrates are still largely unknown. Structural knowledge of the human serotonin transporter (hSERT) is much awaited for understanding the mechanistic details of substrate translocation and binding of antidepressants and drugs of abuse. The publication of the crystal structure of the homologous leucine transporter has resulted in homology models of the monoamine transporters. Here we present extended molecular dynamics simulations of an experimentally supported homology model of hSERT with and without the natural substrate yielding a total of more than 1.5 µs of simulation of the protein dimer. The simulations reveal a transition of hSERT from an outward-facing occluded conformation to an inward-facing conformation in a one-substrate-bound state. Simulations with a second substrate in the proposed symport effector site did not lead to conformational changes associated with translocation. The central substrate binding site becomes fully exposed to the cytoplasm leaving both the Na(+)-ion in the Na2-site and the substrate in direct contact with the cytoplasm through water interactions. The simulations reveal how sodium is released and show indications of early events of substrate transport. The notion that ion dissociation from the Na2-site drives translocation is supported by experimental studies of a Na2-site mutant. Transmembrane helices (TMs) 1 and 6 are identified as the helices involved in the largest movements during transport.


Assuntos
Modelos Biológicos , Simulação de Dinâmica Molecular , Proteínas da Membrana Plasmática de Transporte de Serotonina/química , Proteínas da Membrana Plasmática de Transporte de Serotonina/metabolismo , Sódio/metabolismo , Sítios de Ligação , Citoplasma/química , Citoplasma/metabolismo , Humanos , Mutagênese Sítio-Dirigida , Mutação , Ligação Proteica , Conformação Proteica , Proteínas da Membrana Plasmática de Transporte de Serotonina/genética , Sódio/química , Água
19.
J Biol Chem ; 285(11): 8363-74, 2010 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-19948720

RESUMO

Tricyclic antidepressants (TCAs) have been used for decades, but their orientation within and molecular interactions with their primary target is yet unsettled. The recent finding of a TCA binding site in the extracellular vestibule of the bacterial leucine transporter 11 A above the central site has prompted debate about whether this vestibular site in the bacterial transporter is applicable to binding of antidepressants to their relevant physiological target, the human serotonin transporter (hSERT). We present an experimentally validated structural model of imipramine and analogous TCAs in the central substrate binding site of hSERT. Two possible binding modes were observed from induced fit docking calculations. We experimentally validated a single binding mode by combining mutagenesis of hSERT with uptake inhibition studies of different TCA analogs according to the paired mutation ligand analog complementation paradigm. Using this experimental method, we identify a salt bridge between the tertiary aliphatic amine and Asp(98). Furthermore, the 7-position of the imipramine ring is found vicinal to Phe(335), and the pocket lined by Ala(173) and Thr(439) is utilized by 3-substituents. These protein-ligand contact points unambiguously orient the TCA within the central binding site and reveal differences between substrate binding and inhibitor binding, giving important clues to the inhibition mechanism. Consonant with the well established competitive inhibition of uptake by TCAs, the resulting binding site for TCAs in hSERT is fully overlapping with the serotonin binding site in hSERT and dissimilar to the low affinity noncompetitive TCA site reported in the leucine transporter (LeuT).


Assuntos
Antidepressivos Tricíclicos/química , Antidepressivos Tricíclicos/metabolismo , Imipramina/química , Imipramina/metabolismo , Proteínas da Membrana Plasmática de Transporte de Serotonina/metabolismo , Alanina/genética , Ácido Aspártico/genética , Sítios de Ligação , Ligação Competitiva , Células Cultivadas , Humanos , Imipramina/análogos & derivados , Rim/citologia , Leucina/genética , Modelos Químicos , Mutagênese Sítio-Dirigida , Fenilalanina/genética , Serotonina/farmacocinética , Proteínas da Membrana Plasmática de Transporte de Serotonina/química , Proteínas da Membrana Plasmática de Transporte de Serotonina/genética , Relação Estrutura-Atividade , Transfecção , Trítio
20.
Org Biomol Chem ; 9(22): 7807-13, 2011 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-21952673

RESUMO

Inhibition of ß-glucuronidases has recently been shown to be useful in alleviating drug toxicity for common colon cancer chemotherapeutic CPT-11 (also called Irinotecan). We have prepared a new compound of the nortropane-type, uronic-Noeurostegine, and demonstrated that this is a competitive and potent E. coli ß-glucuronidase inhibitor, while inhibition of the mammalian ß-glucuronidase from bovine liver was found to be less significant. Although not intended, two other compounds having N-ethyl and N-(4-hydroxybutyl) substituents were also prepared in this study due to the sluggish debenzylation in the final step. The N-substituents are believed to come from reaction with the solvents used being ethanol and THF, respectively. These compounds also inhibited the two ß-glucuronidases albeit to a lesser extent compared to the parent compound. Noeurostegine and the three uronic-noeurostegines were additionally evaluated as inhibitors against a wide panel of glycosidases with the former showing potent inhibition of rat intestinal lactase and trehalase, whereas the latter was found to be inactive.


Assuntos
Química Farmacêutica/métodos , Inibidores Enzimáticos/síntese química , Proteínas de Escherichia coli/antagonistas & inibidores , Glucuronidase/antagonistas & inibidores , Nortropanos/síntese química , Animais , Ligação Competitiva , Bovinos , Inibidores Enzimáticos/farmacologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/enzimologia , Proteínas de Escherichia coli/metabolismo , Glucuronidase/metabolismo , Concentração Inibidora 50 , Intestinos/efeitos dos fármacos , Intestinos/enzimologia , Lactase/metabolismo , Fígado/efeitos dos fármacos , Fígado/enzimologia , Modelos Moleculares , Nortropanos/farmacologia , Ligação Proteica , Ratos , Especificidade da Espécie , Trealase/antagonistas & inibidores , Trealase/metabolismo , Ácidos Urônicos/química
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