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1.
J Enzyme Inhib Med Chem ; 35(1): 289-297, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31797703

RESUMO

In this study, newly synthesised compounds 6, 8, 10 and other compounds (1-5, 7 and 9) and their inhibitory properties against the human isoforms hCA I and hCA II were reported for the first time. Compounds 1-10 showed effective inhibition profiles with KI values in the range of 5.13-16.9 nM for hCA I and of 11.77-67.39 nM against hCA II, respectively. Molecular docking studies were also performed with Glide XP to get insight into the inhibitory activity and to evaluate the binding modes of the synthesised compounds to hCA I and II. More rigorous binding energy calculations using MM-GBSA protocol which agreed well with observed activities were then performed to improve the docking scores. Results of in silico calculations showed that all compounds obey drug likeness properties. The new compounds reported here might be promising lead compounds for the development of new potent inhibitors as alternatives to classical hCA inhibitors.


Assuntos
Anidrase Carbônica II/antagonistas & inibidores , Anidrase Carbônica I/antagonistas & inibidores , Inibidores da Anidrase Carbônica/farmacologia , Desenho de Drogas , Pirazóis/farmacologia , Anidrase Carbônica I/metabolismo , Anidrase Carbônica II/metabolismo , Inibidores da Anidrase Carbônica/síntese química , Inibidores da Anidrase Carbônica/química , Relação Dose-Resposta a Droga , Humanos , Modelos Moleculares , Estrutura Molecular , Pirazóis/síntese química , Pirazóis/química , Relação Estrutura-Atividade
2.
Biophys Chem ; 256: 106276, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31731070

RESUMO

Heme-copper oxidases couple the exergonic oxygen reduction with the endergonic proton translocation. Redox-linked structural changes have been localized in deeply buried regions of the protein, near the low-potential heme. How these movements can modulate distant gating events along the intramolecular proton path, where the entry (exit) of pumped proton occurs, is a major concern for the proton pump models. Generally, these models associate, more or less directly, all translocation events with redox transitions. Although they can account for many phenomenological aspects of the pump, evidences from single-molecules experiments about leak states of the pump represent a formidable challenge. Disconnecting the redox-linked pKa shifts of the proton loading site from the external barriers, we obtain a simple stochastic mechanism which behaves similarly to the real enzyme, able to reverse the flow of the proton transfer.


Assuntos
Heme/química , Oxirredutases/química , Bombas de Próton/química , Animais , Bovinos/metabolismo , Heme/metabolismo , Cinética , Modelos Moleculares , Oxirredução , Oxirredutases/metabolismo , Bombas de Próton/metabolismo
3.
Biosci Biotechnol Biochem ; 84(1): 1-16, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31538538

RESUMO

Recent investigations suggest that soluble oligomeric amyloid ß (Aß) species may be involved in early onset of Alzheimer's disease (AD). Using systematic proline replacement, solid-state NMR, and ESR, we identified a toxic turn at position 22 and 23 of Aß42, the most potent neurotoxic Aß species. Through radicalization, the toxic turn can induce formation of the C-terminal hydrophobic core to obtain putative Aß42 dimers and trimers. Synthesized dimer and trimer models showed that the C-terminal hydrophobic core plays a critical role in the formation of high molecular weight oligomers with neurotoxicity. Accordingly, an anti-toxic turn antibody (24B3) that selectively recognizes a toxic dimer model of E22P-Aß42 was developed. Sandwich enzyme-linked immunosorbent assay with 24B3 and 82E1 detected a significantly higher ratio of Aß42 with a toxic turn to total Aß42 in cerebrospinal fluid of AD patients compared with controls, suggesting that 24B3 could be useful for early onset of AD diagnosis.


Assuntos
Doença de Alzheimer/diagnóstico , Doença de Alzheimer/tratamento farmacológico , Peptídeos beta-Amiloides/líquido cefalorraquidiano , Peptídeos beta-Amiloides/imunologia , Anticorpos Monoclonais/uso terapêutico , Fragmentos de Peptídeos/líquido cefalorraquidiano , Fragmentos de Peptídeos/imunologia , Doença de Alzheimer/líquido cefalorraquidiano , Peptídeos beta-Amiloides/química , Animais , Modelos Animais de Doenças , Ensaio de Imunoadsorção Enzimática , Humanos , Camundongos , Modelos Moleculares , Emaranhados Neurofibrilares/química , Fragmentos de Peptídeos/química , Placa Amiloide/química , Prolina/química , Agregados Proteicos , Agregação Patológica de Proteínas , Estrutura Terciária de Proteína
4.
J Enzyme Inhib Med Chem ; 35(1): 21-30, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-31619095

RESUMO

Trypanosoma cruzi carbonic anhydrase (TcCA) has recently emerged as an interesting target for the design of new compounds to treat Chagas disease. In this study we report the results of a structure-based virtual screening campaign to identify novel and selective TcCA inhibitors. The combination of properly validated computational methodologies such as comparative modelling, molecular dynamics and docking simulations allowed us to find high potency hits, with KI values in the nanomolar range. The compounds also showed trypanocidal effects against T. cruzi epimastigotes and trypomastigotes. All the candidates are selective for inhibiting TcCA over the human isoform CA II, which is encouraging in terms of possible therapeutic safety and efficacy.


Assuntos
Inibidores da Anidrase Carbônica/farmacologia , Anidrases Carbônicas/metabolismo , Doença de Chagas/tratamento farmacológico , Ciclamatos/farmacologia , Tripanossomicidas/farmacologia , Inibidores da Anidrase Carbônica/síntese química , Inibidores da Anidrase Carbônica/química , Doença de Chagas/metabolismo , Ciclamatos/síntese química , Ciclamatos/química , Relação Dose-Resposta a Droga , Avaliação Pré-Clínica de Medicamentos , Humanos , Modelos Moleculares , Estrutura Molecular , Testes de Sensibilidade Parasitária , Relação Estrutura-Atividade , Tripanossomicidas/síntese química , Tripanossomicidas/química , Trypanosoma cruzi/efeitos dos fármacos , Trypanosoma cruzi/enzimologia
5.
J Enzyme Inhib Med Chem ; 35(1): 96-108, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31690133

RESUMO

A series of analogues of Amb639752, a novel diacylglycerol kinase (DGK) inhibitor recently discovered by us via virtual screening, have been tested. The compounds were evaluated as DGK inhibitors on α, θ, and ζ isoforms, and as antagonists on serotonin receptors. From these assays emerged two novel compounds, namely 11 and 20, which with an IC50 respectively of 1.6 and 1.8 µM are the most potent inhibitors of DGKα discovered to date. Both compounds demonstrated the ability to restore apoptosis in a cellular model of X-linked lymphoproliferative disease as well as the capacity to reduce the migration of cancer cells, suggesting their potential utility in preventing metastasis. Finally, relying on experimental biological data, molecular modelling studies allow us to set a three-point pharmacophore model for DGK inhibitors.


Assuntos
Lipase Lipoproteica/antagonistas & inibidores , Inibidores de Proteínas Quinases/farmacologia , Movimento Celular/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Células HEK293 , Humanos , Lipase Lipoproteica/metabolismo , Linfócitos/efeitos dos fármacos , Células MCF-7 , Modelos Moleculares , Estrutura Molecular , Monócitos/efeitos dos fármacos , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Relação Estrutura-Atividade , Linfócitos T/efeitos dos fármacos
6.
J Enzyme Inhib Med Chem ; 35(1): 139-144, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31724435

RESUMO

A series of naphthalene-chalcone derivatives (3a-3t) were prepared and evaluated as tubulin polymerisation inhibitor for the treatment of breast cancer. All compounds were evaluated for their antiproliferative activity against MCF-7 cell line. The most of compounds displayed potent antiproliferative activity. Among them, compound 3a displayed the most potent antiproliferative activity with an IC50 value of 1.42 ± 0.15 µM, as compared to cisplatin (IC50 = 15.24 ± 1.27 µM). Additionally, the promising compound 3a demonstrated relatively lower cytotoxicity on normal cell line (HEK293) compared to tumour cell line. Furthermore, compound 3a was found to induce significant cell cycle arrest at the G2/M phase and cell apoptosis. Compound 3a displayed potent tubulin polymerisation inhibitory activity with an IC50 value of 8.4 µM, which was slightly more active than the reference compound colchicine (IC50 = 10.6 µM). Molecular docking analysis suggested that 3a interact and bind at the colchicine binding site of the tubulin.


Assuntos
Antineoplásicos/farmacologia , Neoplasias da Mama/tratamento farmacológico , Chalconas/farmacologia , Naftalenos/farmacologia , Moduladores de Tubulina/farmacologia , Tubulina (Proteína)/metabolismo , Antineoplásicos/síntese química , Antineoplásicos/química , Apoptose/efeitos dos fármacos , Sítios de Ligação/efeitos dos fármacos , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Pontos de Checagem do Ciclo Celular/efeitos dos fármacos , Proliferação de Células/efeitos dos fármacos , Chalconas/química , Colchicina/antagonistas & inibidores , Colchicina/metabolismo , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Feminino , Humanos , Células MCF-7 , Modelos Moleculares , Estrutura Molecular , Naftalenos/química , Relação Estrutura-Atividade , Moduladores de Tubulina/síntese química , Moduladores de Tubulina/química
7.
J Enzyme Inhib Med Chem ; 35(1): 172-186, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31752564

RESUMO

Sphingosine kinase 1 (SphK1) is a promising therapeutic target against several diseases including mammary cancer. The aim of present work is to identify a potent lead compound against breast cancer using ligand-based virtual screening, molecular docking, MD simulations, and the MMPBSA calculations. The LBVS in molecular and virtual libraries yielded 20,800 hits, which were reduced to 621 by several parameters of drug-likeness, lead-likeness, and PAINS. Furthermore, 55 compounds were selected by ADMET descriptors carried forward for molecular interaction studies with SphK1. The binding energy (ΔG) of three screened compounds namely ZINC06823429 (-11.36 kcal/mol), ZINC95421501 (-11.29 kcal/mol), and ZINC95421070 (-11.26 kcal/mol) exhibited stronger than standard drug PF-543 (-9.9 kcal/mol). Finally, it was observed that the ZINC06823429 binds tightly to catalytic site of SphK1 and remain stable during MD simulations. This study provides a significant understanding of SphK1 inhibitors that can be used in the development of potential therapeutics against breast cancer.


Assuntos
Antineoplásicos/farmacologia , Neoplasias da Mama/tratamento farmacológico , Inibidores Enzimáticos/farmacologia , Fosfotransferases (Aceptor do Grupo Álcool)/antagonistas & inibidores , Antineoplásicos/síntese química , Antineoplásicos/química , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Proliferação de Células/efeitos dos fármacos , Relação Dose-Resposta a Droga , Avaliação Pré-Clínica de Medicamentos , Ensaios de Seleção de Medicamentos Antitumorais , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Humanos , Modelos Moleculares , Estrutura Molecular , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , Relação Estrutura-Atividade
8.
J Phys Chem Lett ; 11(1): 292-296, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31841337

RESUMO

Urea is a strong denaturing osmolyte that disrupts noncovalent bonds in proteins. Here, we present a small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE) study on the structure and dynamics of the intrinsically disordered myelin basic protein (MBP) denatured by urea. SANS results show that urea-denatured MBP is more compact than ideal polymers, while its secondary structure content is entirely lost. NSE experiments reveal concomitantly an increase of the relaxation time and of the amplitude of internal motions in urea-denatured MBP as compared to native MBP. If interpreted in terms of the Zimm model including internal friction (ZIF), the internal friction parameter decreased by a factor of 6.5. Urea seems to not only smooth local energy barriers, reducing internal friction on a local scale, but also significantly reduces the overall depth of the global energy landscape. This leads to a nearly complete loss of restoring forces beyond entropic forces and in turn allows for larger motional amplitudes. Obviously, the noncovalent H-bonds are largely eliminated, driving the unfolded protein to be more similar to a synthetic polymer.


Assuntos
Proteína Básica da Mielina/química , Ureia/química , Fricção , Modelos Moleculares , Difração de Nêutrons , Conformação Proteica , Desnaturação Proteica , Espalhamento a Baixo Ângulo , Software
9.
Chemosphere ; 238: 124466, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31425866

RESUMO

Arsenite is a highly toxic compound present in many water sources around the world. The removal of arsenite from water requires its oxidation to arsenate which is much more amenable to treatment using well attested technologies. Prior research has shown that the oxidation of arsenite by hydroxyl radicals is significantly accelerated in the presence of carbonate ions but the intrinsic mechanisms of the acceleration have not yet been established. The main goal of the present work was to examine the oxidation of arsenite in the framework of the density functional theory, to establish a detailed microscopic level mechanism of interactions between arsenite and hydroxyl radicals and to elucidate the nature of the catalytic effect of carbonate ions. Results of this study demonstrate that the [As(OH)2CO3]- complex is the thermodynamically most stable species formed in the system H3AsO3-CO32-/HCO3--H2O. Interactions of the hydroxyl radical with the [As(OH)2CO3]- complex yield the pre-reaction complex [As(OH)3CO3]-∗ in the reaction of subsequent oxidation of arsenite. The structures of the reactants, products and transition states, as well as pre- and post-reaction complexes corresponding to several possible mechanisms of the first stage of As(III) oxidation to As(IV) intermediate using hydroxyl radicals in the absence and in the presence of [As(OH)2CO3]-, were determined in this study. The data demonstrate that the arsenite-carbonate complexes [As(OH)2CO3]- are characterized by a significantly lower activation energy of the first oxidation stage under the action of a hydroxyl radical (2.8 kcal/mol) compared to that for the free arsenite H3AsO3 (13.6 kcal/mol).


Assuntos
Arsenitos/química , Carbonatos/química , Radical Hidroxila/química , Teoria Quântica , Água/química , Catálise , Modelos Moleculares , Conformação Molecular , Oxirredução , Termodinâmica
10.
Food Chem ; 308: 125596, 2020 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-31648097

RESUMO

The protective mechanism of glycerol on ß-lactoglobulin were studied in 0-60% glycerol solutions by experimental and molecular simulation approaches. Results showed that the stability of ß-lactoglobulin increased with glycerol concentration, with little secondary structure changes induced by glycerol. The tertiary structure altered slightly with glycerol concentration, resulting in a stronger near UV circular dichroism signal and intrinsic tryptophan fluorescence quenching, indicating aromatic side chains closer to hydrophobic microenvironment. The Rg of ß-lactoglobulin increased with glycerol concentration without dimer dissociation, due to expansion of the quaternary structures. Moreover, the flexibility (RMSF) of ß-lactoglobulin decreased by glycerol. Distance between areas enclosing Asp33 and Arg40 from separate chains did not increase, suggesting possibly reinforced electrostatic attractions. In conclusion, the stabilization of ß-lactoglobulin in glycerol solution is probably the comprehensive results of the decreased molecular flexibility, the strengthened hydrophobic interaction in individual chain, and the possibly reinforced electrostatic attractions between two chains of ß-lactoglobulin.


Assuntos
Glicerol/química , Lactoglobulinas/química , Dicroísmo Circular , Interações Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína
11.
J Colloid Interface Sci ; 559: 1-12, 2020 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-31605780

RESUMO

Experimental and computational approaches are utilized to investigate the influence of electrostatic fields on the binding force between human coagulation protein thrombin and its DNA aptamer. The thiolated aptamer was deposited onto gold substrate located in a liquid cell filled with binding buffer, then the thrombin-functionalized atomic force microscopy (AFM) probe was repeatedly brought into contact with the aptamer-coated surface under applied electrical potentials of -100, 0, and 100 mV respectively. Force drops during the pull-off process were measured to determine the unbinding forces between thrombin and aptamer in a range of loading rates spanning from ~3 × 102 to ~1 × 104 pN/s. The results from experiments showed that both of the binding strength and propensity of the complex are drastically diminished under positive electrode potential, whereas there is no influence on the molecular binding from negative electrode potential. We also used a theoretical analysis to explain the nature of electrostatic potential and field inside the aptamer-thrombin layer, which in turn could quantify the influence of the electrostatically repulsive force on a thrombin molecule that promotes dissociation from the aptamer due to positive electrode potential, and achieve good agreement with the experimental results. The study confirms the feasibility of electrostatic modulation upon the binding interaction between thrombin and aptamer, and implicates an underlying application perspective upon nanoscale manipulation of the stimuli responsive biointerface.


Assuntos
Aptâmeros de Nucleotídeos/química , Trombina/química , Técnicas Biossensoriais/métodos , Eletricidade , Técnicas Eletroquímicas/métodos , Eletrodos , Ouro/química , Fenômenos Mecânicos , Modelos Moleculares , Ligação Proteica , Eletricidade Estática , Propriedades de Superfície
12.
J Enzyme Inhib Med Chem ; 34(1): 1573-1589, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31852269

RESUMO

Pyridazine scaffolds are considered privileged structures pertaining to its novelty, chemical stability, and synthetic feasibility. In our quest towards the development of novel scaffolds for effective vascular endothelial growth 2 (VEGFR-2) inhibition with antiangiogenic activity, four novel series of pyridazines were designed and synthesised. Five of the synthesised compounds; namely (8c, 8f, 15, 18b, and 18c) exhibited potent VEGFR-2 inhibitory potency (>80%); with IC50 values ranging from low micromolar to nanomolar range; namely compounds 8c, 8f, 15, 18c with (1.8 µM, 1.3 µM, 1.4 µM, 107 nM), respectively. Moreover, 3-[4-{(6-oxo-1,6-dihydropyridazin-3-yl)oxy}phenyl]urea derivative (18b) exhibited nanomolar potency towards VEGFR-2 (60.7 nM). In cellular assay, the above compounds showed excellent inhibition of VEGF-stimulated proliferation of human umbilical vein endothelial cells at 10 µM concentration. Finally, an extensive molecular simulation study was performed to investigate the probable interaction with VEGFR-2.


Assuntos
Antineoplásicos/farmacologia , Descoberta de Drogas , Inibidores de Proteínas Quinases/farmacologia , Piridazinas/farmacologia , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Antineoplásicos/síntese química , Antineoplásicos/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Teoria da Densidade Funcional , Ensaios de Seleção de Medicamentos Antitumorais , Células Endoteliais da Veia Umbilical Humana/efeitos dos fármacos , Humanos , Modelos Moleculares , Estrutura Molecular , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Piridazinas/síntese química , Piridazinas/química , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo
13.
J Enzyme Inhib Med Chem ; 34(1): 712-727, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31852270

RESUMO

The design of multi-target directed ligands (MTDLs) is a valid approach for obtaining effective drugs for complex pathologies. MTDLs that combine neuro-repair properties and block the first steps of neurotoxic cascades could be the so long wanted remedies to treat neurodegenerative diseases (NDs). By linking two privileged scaffolds with well-known activities in ND-targets, the flavonoid and the N,N-dibenzyl(N-methyl)amine (DBMA) fragments, new CNS-permeable flavonoid - DBMA hybrids (1-13) were obtained. They were subjected to biological evaluation in a battery of targets involved in Alzheimer's disease (AD) and other NDs, namely human cholinesterases (hAChE/hBuChE), ß-secretase (hBACE-1), monoamine oxidases (hMAO-A/B), lipoxygenase-5 (hLOX-5) and sigma receptors (σ1R/σ2R). After a funnel-type screening, 6,7-dimethoxychromone - DBMA (6) was highlighted due to its neurogenic properties and an interesting MTD-profile in hAChE, hLOX-5, hBACE-1 and σ1R. Molecular dynamic simulations showed the most relevant drug-protein interactions of hybrid 6, which could synergistically contribute to neuronal regeneration and block neurodegeneration.


Assuntos
Doença de Alzheimer/tratamento farmacológico , Inibidores Enzimáticos/farmacologia , Flavonoides/farmacologia , Metilaminas/farmacologia , Regeneração Nervosa/efeitos dos fármacos , Fármacos Neuroprotetores/farmacologia , Acetilcolinesterase/metabolismo , Doença de Alzheimer/metabolismo , Secretases da Proteína Precursora do Amiloide/antagonistas & inibidores , Secretases da Proteína Precursora do Amiloide/metabolismo , Animais , Araquidonato 5-Lipoxigenase/metabolismo , Ácido Aspártico Endopeptidases/antagonistas & inibidores , Ácido Aspártico Endopeptidases/metabolismo , Barreira Hematoencefálica/efeitos dos fármacos , Barreira Hematoencefálica/metabolismo , Butirilcolinesterase/metabolismo , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Flavonoides/química , Humanos , Masculino , Metilaminas/química , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Modelos Moleculares , Estrutura Molecular , Monoaminoxidase/metabolismo , Fármacos Neuroprotetores/síntese química , Fármacos Neuroprotetores/química
14.
J Chem Phys ; 151(23): 230902, 2019 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-31864250

RESUMO

Polymeric materials are ubiquitous in our daily lives, and they play a significant role in many technological applications. The general predictive framework for the behavior of soft polymeric materials can be divided into two vastly different approaches. Highly coarse-grained models capture polymers as flexible random walks, resulting in general predictions of physical behavior but lack chemical specificity. Detailed atomistic models contain molecular detail but are frequently computationally intractable for exhaustive materials discovery. In this perspective, we discuss theoretical models that successfully bridge these disparate approaches. We identify intermediate-scale physical models that are amenable to theoretical analyses while containing sufficient granular detail to capture a range of molecular-level processes. We then provide several problems in materials engineering and biological physics where multiscale physics is essential in their behavior.


Assuntos
DNA/química , Polímeros/química , Humanos , Modelos Moleculares
15.
Phys Rev Lett ; 123(23): 238102, 2019 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-31868483

RESUMO

Collagen consists of three peptides twisted together through a periodic array of hydrogen bonds. Here we use this as inspiration to find design rules for programmed specific interactions for self-assembling synthetic collagenlike triple helices, starting from disordered configurations. The assembly generically nucleates defects in the triple helix, the characteristics of which can be manipulated by spatially varying the enthalpy of helix formation. Defect formation slows assembly, evoking kinetic pathologies that have been observed to mutations in the primary collagen amino acid sequence. The controlled formation and interaction between defects gives a route for hierarchical self-assembly of bundles of twisted filaments.


Assuntos
Colágeno/química , Modelos Químicos , Sequência de Aminoácidos , Modelos Moleculares , Nanoestruturas/química , Peptídeos/química , Conformação Proteica em alfa-Hélice
16.
Phys Chem Chem Phys ; 21(44): 24601-24619, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31670335

RESUMO

Natural bond orbital (NBO) analysis of electron delocalization in a series of capped isolated peptides is used to diagnose amide-amide H-bonding and backbone-induced hyperconjugative interactions, and to rationalize their spectral effects. The sum of the stabilization energies corresponding to the interactions between NBOs that are involved in the H-bonding is demonstrated as an insightful indicator for the H-bond strength. It is then used to decouple the effect of the H-bond distance from that, intrinsic, of the donor/acceptor relative orientation, i.e., the geometrical approach. The diversity of the approaches given by the series of peptides studied enables us to illustrate the crucial importance of the approach when the acceptor is a carbonyl group, and emphasizes that efficient approaches can be achieved despite not matching the usual picture of a proton donor directly facing a lone pair of the proton acceptor, i.e., that encountered in intermolecular H-bonds. The study also illustrates the role of backbone flexibility, partly controlled by backbone-amide hyperconjugative interactions, in influencing the equilibrium structures, in particular by frustrating or enhancing the HB for a given geometrical approach. Finally, the presently used NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor amide NH stretching mode, but this simple picture is blurred by ubiquitous hyperconjugative effects between the backbone and amide groups, whose magnitude can be comparable to that of the weakest H-bonds.


Assuntos
Amidas/química , Peptídeos/química , Dimerização , Ligações de Hidrogênio , Modelos Moleculares , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Teoria Quântica
17.
Phys Chem Chem Phys ; 21(45): 25290-25301, 2019 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-31701097

RESUMO

The voltage-gated potassium channel Kv4.3 plays a vital role in shaping the timing, frequency, and backpropagation of electrical signals in the brain and heart by generating fast transient currents at subthreshold membrane potentials in repetitive firing neurons. To achieve its physiological function, Kv4.3 is assisted by auxiliary ß-subunits that become integral parts of the native A-type potassium channels, among which there are the Kv channel-interacting proteins (KChIPs). KChIPs are a family of cytosolic proteins that, when coexpressed with Kv4, lead to higher current density, modulation of channel inactivation and faster recovery from inactivation, while the loss of KChIP function may lead to severe pathological states. Recently, the structural basis of the KChIP1-Kv4.3 interaction was reported by using two similar X-ray crystallographic structures, which supported a crucial role for KChIP1 in enhancing the stability of the Kv4.3 tetrameric assembly, thus helping the trafficking of the channel to the plasma membrane. Here, we investigate through fully atomistic simulations the structure and stability of the human Kv4.3 tetramerization (T1) domain in complex with KChIP1 upon specific mutations located in the first and second interfaces of the complex, as compared to the wild-type (WT). Our results nicely complement the available structural and biophysical information collected so far on these complex variants. In particular, the degree of structural deviations and energetic instability, from small to substantial, observed in these variants with respect to the WT model seems to parallel well the level of channel dysfunction known from electrophysiology data. Our simulations provide an octameric structure of the WT KChIP1-Kv4.3 assembly very similar to the known crystal structures, and, at the same time, highlight the importance of a previously overlooked site of interaction between KChIP1 and the Kv4.3 T1 domain.


Assuntos
Simulação por Computador , Proteínas Interatuantes com Canais de Kv/química , Canais de Potássio Shal/química , Cristalografia por Raios X , Humanos , Proteínas Interatuantes com Canais de Kv/genética , Modelos Moleculares , Mutação , Canais de Potássio Shal/genética
18.
J Chem Phys ; 151(18): 185105, 2019 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-31731855

RESUMO

Force spectroscopy techniques are often used to learn about the free energy landscape of single biomolecules, typically by recovering free energy quantities that, extrapolated to zero force, are compared to those measured in bulk experiments. However, it is not always clear how the information obtained from a mechanically perturbed system can be related to the information obtained using other denaturants since tensioned molecules unfold and refold along a reaction coordinate imposed by the force, which is not likely to be meaningful in its absence. Here, we explore this dichotomy by investigating the unfolding landscape of a model protein, which is unfolded first mechanically through typical force spectroscopy-like protocols and next thermally. When unfolded by nonequilibrium force extension and constant force protocols, we recover a simple two-barrier landscape as the protein reaches the extended conformation through a metastable intermediate. Interestingly, folding-unfolding equilibrium simulations at low forces suggested a totally different scenario, where this metastable state plays little role in the unfolding mechanism, and the protein unfolds through two competing pathways [R. Tapia-Rojo et al., J. Chem. Phys. 141, 135102 (2014)]. Finally, we use Markov state models to describe the configurational space of the unperturbed protein close to the critical temperature. The thermal dynamics is well understood by a one-dimensional landscape along an appropriate reaction coordinate, however it is very different from the mechanical picture. In this sense, the results of our protein model for the mechanical and thermal descriptions provide incompatible views of the folding/unfolding landscape of the system, and the estimated quantities to zero force result are hard to interpret.


Assuntos
Desdobramento de Proteína , Proteínas/química , Temperatura Ambiente , Cadeias de Markov , Fenômenos Mecânicos , Modelos Moleculares , Conformação Proteica
19.
J Chem Phys ; 151(19): 195101, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31757137

RESUMO

The solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect has been studied in a quinone-depleted uniformly (u-)13C,15N-labeled photosynthetic reaction center (RC) protein from purple bacterium Rhodobacter (R.) sphaeroides wild type (WT). As a method for investigation, solid-state 15N NMR under magic-angle spinning (MAS) is applied under both continuous illumination (steady state) and nanosecond-laser flashes (time-resolved). While all previous 15N photo-CIDNP MAS NMR studies on the purple bacterial RC used the carotenoid-less mutant R26, this is the first using WT samples. The absence of further photo-CIDNP mechanisms (compared to R26) and various couplings (compared to 13C NMR experiments on 13C-labeled samples) allows the simplification of the spin-system. We report 15N signals of the three cofactors forming the spin-correlated radical pair (SCRP) and, based on density-functional theory calculations, their assignment. The simulation of photo-CIDNP intensities and time-resolved 15N photo-CIDNP MAS NMR data matches well to the frame of the mechanistic interpretation. Three spin-chemical processes, namely, radical pair mechanism, three spin mixing, and differential decay, generate emissive (negative) 15N polarization in the singlet decay channel and absorptive (positive) polarization in the triplet decay channel of the SCRP. The absorptive 15N polarization of the triplet decay channel is transiently obscured during the lifetime of the triplet state of the carotenoid (3Car); therefore, the observed 15N signals are strongly emissive. Upon decay of 3Car, the transiently obscured polarization becomes visible by reducing the excess of emissive polarization. After the decline of 3Car, the remaining nuclear hyperpolarization decays with nuclear T1 relaxation kinetics.


Assuntos
Ressonância Magnética Nuclear Biomolecular , Complexo de Proteínas do Centro de Reação Fotossintética/química , Rhodobacter sphaeroides/metabolismo , Modelos Moleculares , Complexo de Proteínas do Centro de Reação Fotossintética/metabolismo , Conformação Proteica
20.
J Phys Chem Lett ; 10(22): 7200-7207, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31693374

RESUMO

DNA compaction is essential to ensure the packaging of the genetic material in living cells and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, DNA packaging is achieved by specific well-conserved proteins. Here, by means of all-atom molecular dynamics simulations, including the determination of relevant free-energy profiles, we rationalize the molecular bases for this remarkable process in bacteria, illustrating the crucial role played by positively charged amino acids of a small histone-like protein. We also present compelling evidence that this histone-like protein alone can induce strong bending of a DNA duplex around its core domain, a process that requires overcoming a major free-energy barrier.


Assuntos
Proteínas de Bactérias/química , Borrelia burgdorferi/química , Empacotamento do DNA , DNA Bacteriano/química , Histonas/química , Simulação de Dinâmica Molecular , Modelos Moleculares
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