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1.
Small Methods ; 8(3): e2300816, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37926773

RESUMO

The spin states of active sites have a significant impact on the adsorption/desorption ability of the reaction intermediates during the oxygen evolution reaction (OER). Sulfide spinel is not generally considered a highly efficient OER catalyst owing to the low spin state of Co3+ and the lack of unpaired electrons available for adsorption of reaction intermediates. Herein, it is proposed a novel Nd-evoked valence electronic adjustment strategy to engineer the spin state of Co ions. The unique f-p-d orbital electronic coupling effect stimulates the rearrangement of Co d orbital electrons and increases the eg electron filling to achieve high-spin state Co ions, which promotes charge transport by propagating a spin channel and generates a high number of active sites for intermediate adsorption. The optimized CuCo1.75 Nd0.25 S4 catalyst exhibits outstanding electrocatalytic properties with a low overpotential of 320 mV at 500 mA cm-2 and a 48 h stability at 300 mA cm-2 . In situ synchrotron radiation infrared spectra confirm the quick accumulation of key *OOH and *O intermediates. This work deepens the comprehensive understanding of the relationship between OER activity and spin configurations of Co ions and offers a new design strategy for spinel compound catalysts.

2.
Molecules ; 28(21)2023 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-37959777

RESUMO

Equilibrium geometries and properties of self-assembled (InN)12n (n = 1-9) nanoclusters (nanowires and nanosheets) are studied using the GGA-PBE (general gradient approximation with Perdew-Burke-Ernzerh) method. The relative stabilities and growth patterns of semiconductor (InN)12n nanoclusters are investigated. The odd-numbered nano-size (InN)12n (n is odd) have weaker stabilities compared with the neighboring even-numbered (InN)12n (n is even) ones. The most stable (InN)48 nanosheet is selected as a building unit for self-assembled nano-size film materials. In particular, the energy gaps of InN nanoclusters show an even-odd oscillation and reflect that (InN)12n (n = 1-9) nanoclusters are good optoelectronic materials and nanodevices due to their energy gaps in the visible region. Interestingly, the calculated energy gaps for (InN)12n nanowires varies slightly compared with that of individual (InN)12 units. Additionally, the predicted natural atomic populations of In atoms in (InN)12n nanoclusters show that the stabilities of (InN)12n nanoclusters is enhanced through the ionic bonding and covalent bonding of (InN)12n (n = 1-9) nanoclusters.

3.
Chem Commun (Camb) ; 59(64): 9706-9709, 2023 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-37470085

RESUMO

A telluride-spinel ZnCo2Te4/NF catalyst delivered an overpotential (η) of only 370 mV to achieve a current density of 100 mA cm-2 and displayed no significant degradation of performance during 50 h of operation. By virtue of in situ synchrotron infrared spectroscopic detection, an accumulation of key OOH* intermediates over the active site was observed, suggesting that the reaction followed the efficient adsorbate evolution mechanism (AEM) for water oxidation.

4.
ACS Appl Mater Interfaces ; 14(9): 11567-11574, 2022 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-35209715

RESUMO

The combination of Cu and Ag presents a promising way to steer the CO2 reduction products through regulating the surface active sites. However, the difficulty in forming the CuAg alloy with a controllable atomic ratio impedes the in-depth understanding of the structure-activity relationship of CuAg catalysts. Herein, we use E-beam evaporation to synthesize a series of CuAg films with uniform distribution and controllable stoichiometry to reveal the real reaction mechanism on CuAg for the electrochemical CO2 reduction process. Compared with Cu, the Cu1-xAgx (x = 0.05-0.2) alloy showed an apparent suppression of HCOOH and the ratio between C2 liquid products (e.g., ethanol and acetate) and C1 liquid product (HCOOH) is also increased. Operando synchrotron radiation Fourier transform infrared spectroscopy results suggest that the introduction of Ag into the Cu phase can significantly strengthen the absorbed *CO and *OCCO intermediates and suppress the O-C-O intermediates. This research provides a reliable way to inhibit the generation of HCOOH and enhance the production of liquid C2 products during CO2RR and presents a guideline for the future manipulation of copper catalysts by alloying.

5.
Phys Chem Chem Phys ; 21(45): 25302-25310, 2019 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-31701100

RESUMO

The geometries and electronic properties of (SiB)2n (n = 6-27, 30) clusters are systematically investigated based on the gradient corrected Perdew-Burke-Ernzerhof exchange-correlation functional. In particular, the (SiB)36 cage is identified as the most stable nanocluster and (SiB)2n (n = 6-27, 30) nanocages prefer to have sphere-like geometries. By increasing the (SiB)2n (n = 6-27, 30) nanocage size, the calculated energy gaps of (SiB)2n (n = 6-27, 30) nanocages generally decrease and absorption wavelengths of the spectra of (SiB)2n (n = 6-27, 30) nanoclusters are elongated. The varied size of the nanoclusters leads to a quantum confinement effect indirectly. Interestingly, the nanosized (SiB)30-60 cages exhibit a stronger capacity for solar energy absorption or conversion due to both narrow HOMO-LUMO energy gaps and a large DOS near LUMO and HOMO levels. Finally, electronic charges transferred from silicon atoms to their surrounding boron atoms in (SiB)2n (n = 6-27, 30) contribute to the metallic characteristic and B-Si ionic bonds, and eventually enhance the stabilities of the nanocages.

6.
Phys Chem Chem Phys ; 21(47): 26262, 2019 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-31746871

RESUMO

Correction for 'A theoretical study of the geometries, and electronic and surface properties of sphere-like (SiB)2n (n = 6-27, 30) functional nanomaterials' by Run-Ning Zhao et al., Phys. Chem. Chem. Phys., 2019, DOI: 10.1039/c9cp04900b.

7.
J Biomol Struct Dyn ; 36(4): 1009-1028, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28298161

RESUMO

Ebola viruses (EBOV) will induce acute hemorrhagic fever, which is fatal to humans and nonhuman primates. The combination of EBOV VP35 peptide with nucleoprotein N-terminal (NPNTD) is proposed based on static crystal structures in recent studies, but VP35 binding mechanism and conformational dynamics are still unclear. This investigation, using Molecular Dynamic (MD) simulation and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation, more convincingly proves the greater roles of the protein binding mechanisms than do hints from the static crystal structure observations. Conformational analysis of the systems demonstrate that combination with VP35 may lead to the conformational transition of NPNTD from "open" to "closed" state. According to the analyses of binding free energies and their decomposition, VP35 residue R37 plays a crucial role in wild type as well as mutant systems. Mutations of I29 and L33 to aspartate as well as M34 to proline affect binding affinity mainly through influencing electrostatic interaction, which is closely related to H-bonds formation. In addition, mutations mainly affect ß-hairpin and loop regions, among which, M34P may have the greatest influence to the binding. This study may provide specific binding mechanisms between VP35 peptide and NPNTD, especially some important residues concerning binding.


Assuntos
Ebolavirus/química , Doença pelo Vírus Ebola/virologia , Nucleoproteínas/química , Peptídeos/química , Proteínas do Core Viral/química , Sítios de Ligação , Cristalografia por Raios X , Ebolavirus/genética , Doença pelo Vírus Ebola/genética , Humanos , Simulação de Dinâmica Molecular , Proteínas do Nucleocapsídeo , Nucleoproteínas/genética , Ligação Proteica , Conformação Proteica , Proteínas do Core Viral/genética
8.
Mol Biosyst ; 13(5): 1031-1045, 2017 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-28418440

RESUMO

Ebola virus (EBOV) is highly lethal due to virally encoded immune antagonists, and the combination of EBOV VP24 with karyopherin alpha (KPNA) will trigger anti-interferon (IFN) signaling. The crystal structure of VP24-KPNA5 has been proposed in recent studies, but the precise binding mechanisms are still unclear. In order to explore the VP24-KPNA5 protein binding micro-mechanisms, Molecular Dynamic (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation are performed. The obtained results show that EBOV VP24 binding to KPNA5 will rigidify their binding-face, and both proteins will be compacted during binding. According to the analyses of binding free energies of WT and the eight mutant systems, MUT3 makes the most effective contributions to the interaction; additionally MUT4, R398A and the double mutant have the second most effective influence. Hydrogen bond analysis demonstrates that inhibitors which can interfere with the formation of hydrogen bonds D480-T138, E483-R137 and D205-R396 will prevent the anti-IFN effect. Meanwhile, by combining the decomposition of binding free energies (DC) with computational alanine scanning (CAS) results, it is shown that VP24 residues R137 and T138 will be potential targets for EBOV VP24 inhibitors, and KPNA5 residues R396, R398, R480, Y477 and F484 will be potential targets to prevent KPNA5 binding to VP24, which will ultimately block anti-IFN signaling. Our investigations provide theoretical data to understand the binding modes of VP24-KPNA5. The precise binding mechanisms of the complex may shed light on the development of potential novel inhibitors against EBOV infection.


Assuntos
Proteínas Virais/química , Proteínas Virais/metabolismo , alfa Carioferinas/química , alfa Carioferinas/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Ebolavirus/metabolismo , Ligação de Hidrogênio , Interferon beta/metabolismo , Modelos Moleculares , Simulação de Dinâmica Molecular , Mutação , Ligação Proteica , Transdução de Sinais , Proteínas Virais/genética , alfa Carioferinas/genética
9.
Proteins ; 85(6): 1008-1023, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28205249

RESUMO

Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation. R312A/R322A double mutations results in a completely different binding site and orientation upon the structure analyses. The calculated binding free energy results reveal that R312A, R322A, and K339A single mutations decrease the binding free energies by 17.82, 13.18, and 13.68 kcal mol-1 , respectively. The binding energy decomposition indicates that the strong binding affinity of the key residues is mainly due to the contributions of electrostatic interactions in the gas phase, where come from the positively charged side chain and the negatively charged dsRNA backbone. R312A, R322A, and K339A single mutations have no significant effect on VP35 IID conformation, but the mutations influence the contributions of electrostatic interactions in the gas phase. The calculated results reveal that end-cap residues which mainly contribute VDW interactions can recognize and capture dsRNA blunt ends, and the central basic residues (R312, R322, and K339) which mainly contribute favorable electrostatic interactions with dsRNA backbone can fix dsRNA binding site and orientation. Proteins 2017; 85:1008-1023. © 2017 Wiley Periodicals, Inc.


Assuntos
Alanina/química , Substituição de Aminoácidos , Arginina/química , Ebolavirus/química , Simulação de Dinâmica Molecular , RNA de Cadeia Dupla/química , Proteínas Virais Reguladoras e Acessórias/química , Alanina/metabolismo , Arginina/metabolismo , Sítios de Ligação , Interações Hospedeiro-Patógeno , Mutação , Conformação de Ácido Nucleico , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , RNA de Cadeia Dupla/metabolismo , Eletricidade Estática , Termodinâmica , Proteínas Virais Reguladoras e Acessórias/metabolismo
10.
J Biol Phys ; 43(1): 149-165, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28110448

RESUMO

VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP. Interestingly, the sites and orientations of the SWCNT binding to the I295A mutant and K248A/I295A double mutants change significantly to accommodate the variation of the VP35 conformation. Moreover, the VDW can provide the major forces for affinity binding in all four systems.


Assuntos
Simulação de Dinâmica Molecular , Mutação , Nanotubos de Carbono , Proteínas Virais Reguladoras e Acessórias/química , Proteínas Virais Reguladoras e Acessórias/metabolismo , Ligação Proteica , Conformação Proteica , Termodinâmica , Proteínas Virais Reguladoras e Acessórias/genética
11.
J Biomol Struct Dyn ; 34(3): 517-28, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-25933061

RESUMO

Tankyrases (TNKSs), a member of human poly (ADP-ribose) polymerase (PARP) protein superfamily, plays a key role in regulation of cell proliferation. Among the representative proteins of the PARPs family, it is found that the inhibitors have high selectivity for Tankyrase1 (TNKS1). The specific binding modes are investigated between the TNKS1 protein and nicotinamide isostere (ISX) which functions as an inhibitor of TNKS1. The stabilities of ISX-TNKS1 and AVA939-TNKS1 complexes are estimated by molecular dynamics (MD) simulations and free energy calculations; a good agreement with experimental results is reached. On the basis of the calculated results of MD simulations, we found that the inhibitors influence the conformational flexibility of TNKS1 and the XAV939 binding drive the peptide Ile1228-Gly1229-Gly1230 to form a helical structure while the ISX binding drive the peptide to form a turn structure. Moreover, the formed important hydrogen bonds of Tyr1203 residue with XVA939 and WAT1551 with ISX enhance stabilities of the complexes, and the electrostatic interactions in XAV939-TNKS1 and van der Waals interactions in ISX-TNKS1 system are main driving forces for affinity. According to the results of the decomposition of binding free energy, it is obvious that the residues Try1224 and Lys1220 make the most favorable contributions to the binding in, respectively, ISX and XAV939 complexes. Taken together, the obtained results are useful for studying the binding mechanisms of TNKSs and inhibitors and for designing potent inhibitors.


Assuntos
Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Niacinamida/química , Tanquirases/química , Algoritmos , Sítios de Ligação , Domínio Catalítico , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Compostos Heterocíclicos com 3 Anéis/química , Compostos Heterocíclicos com 3 Anéis/farmacologia , Ligação de Hidrogênio , Conformação Molecular , Niacinamida/metabolismo , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Tanquirases/antagonistas & inibidores , Tanquirases/metabolismo
12.
J Comput Aided Mol Des ; 29(12): 1123-36, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26564143

RESUMO

Macrolide biosensor protein MphR(A) has been known as a key regulatory protein in metabolite sensing and genetic expression regulating. MphR(A) protein binds to macrolide antibiotic erythromycin (Ery) and releases the gene operon, thus activates expression of the mphA gene and initiates Ery resistance. The two mutant amino acid residues (V66L and V126L) might potentially disrupt Ery binding to MphR(A). In these studies, the binding of macrolide antibiotic Ery to wild type (Wt) MphR(A) and double mutant (V66L/V126L) MphR(A) are explored by molecular dynamics simulations. Compared to the Apo-MphR(A) protein and Wt-MphR(A)-Ery complex, many interesting effects owing to the double mutant (V66L/V126L) are discovered. In the case of Ery, Helix I which plays an important role in transcription shows itself a right-hand α helix in Wt-MphR(A)-Ery, whereas the activated helix is broken down in double mutant-V66L/V126L-MphR(A)-Ery. The calculated results exhibit that the double mutant V66L/V126L reduces the binding affinity of the V66L/V126L-MphR(A) to Ery, resulting in the block of Ery resistance. The binding free energy decomposition analysis reveals that the decrease of the binding affinity for the variant V66L/V126L-MphR(A)-Ery is mainly attributed to the gas phase electrostatic energies. The residue Leu66, Thr154, and Arg122 enhance the binding affinity of V66L/V126L-MphR(A) to Ery. The residues Tyr103 and His147 contributes mainly to binding energies in the Wt-MphR(A)-Ery complex, whereas the two residues have no contribution to the binding free energy inV66L/V126L-MphR(A)-Ery complex. Our study gives useful insights into the nature of amino acids mutation effect, the mechanism of blocking drug resistance at the atomic level and the characteristics in binding affinity for Ery to double mutant (V66L/V126L) MphR(A), which will contribute to the design of more effective macrolide antibiotics.


Assuntos
Antibacterianos/farmacologia , Resistência Microbiana a Medicamentos , Eritromicina/farmacologia , Infecções por Escherichia coli/tratamento farmacológico , Proteínas de Escherichia coli/metabolismo , Escherichia coli/efeitos dos fármacos , Fatores de Transcrição/metabolismo , Antibacterianos/química , Eritromicina/química , Escherichia coli/química , Escherichia coli/genética , Escherichia coli/metabolismo , Infecções por Escherichia coli/microbiologia , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Humanos , Simulação de Dinâmica Molecular , Mutação Puntual , Ligação Proteica , Estrutura Secundária de Proteína , Termodinâmica , Fatores de Transcrição/química , Fatores de Transcrição/genética
13.
Proteins ; 83(12): 2263-78, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26466951

RESUMO

Ebola viruses (EBOVs) cause an acute and serious illness which is often fatal if untreated, and there is no effective vaccine until now. Multifunctional VP35 is critical for viral replication, RNA silencing suppression and nucleocapsid formation, and it is considered as a future target for the molecular biology technique. In the present work, the binding of inhibitor pyrrole-based compounds (GA017) to wild-type (WT), single (K248A, K251A, and I295A), and double (K248A/I295A) mutant VP35 were investigated by all-atom molecular dynamic (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculation. The calculated results indicate that the binding with GA017 makes the binding pocket more stable and reduces the space of the binding pocket. Moreover, the electrostatic interactions (ΔEele) and VDW energy (ΔEvdw) provide the major forces for affinity binding, and single mutation I295A and double mutation K248A/I295A have great influence on the conformation of the VP35 binding pocket. Interestingly, the residues R300-G301-D302 of I295A form a new helix and the sheet formed by the residues V294-I295-H296-I297 disappears in the double mutation K248A/I295A as compared with WT. Moreover, the binding free energy calculations show that I295A and K248A/I295A mutations decrease of absolute binding free energies while K248A and K251A mutations increase absolute binding free energy. Our calculated results are in good agreement with the experimental results that K248A/I295A double mutant results in near-complete loss of compound binding. The obtained information will be useful for design effective inhibitors for treating Ebola virus.


Assuntos
Antivirais/metabolismo , Proteínas Virais Reguladoras e Acessórias/antagonistas & inibidores , Proteínas Virais Reguladoras e Acessórias/química , Antivirais/química , Sítios de Ligação , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Mutação , Conformação Proteica , Pirróis/química , Pirróis/farmacologia , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/metabolismo , Proteínas Virais Reguladoras e Acessórias/genética , Proteínas Virais Reguladoras e Acessórias/metabolismo
14.
J Biomol Struct Dyn ; 33(5): 946-60, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-24824824

RESUMO

Lassa virus (LASV), an arenavirus known to be responsible for a severe hemorrhagic fever, causes thousands of deaths annually and there is no effective vaccine for it so far. The nucleoprotein (NP) of LASV plays an essential role in the replication and transcription of the viral genome. Recent research shows that viral RNA binds in a deep crevice located within the N-terminal domain of NP and suggests a gating mechanism in which NP transforms from a "closed" position to an "open" position to bind RNA. To characterize the molecular mechanisms of how RNA binds to N-terminal domain of NP, two molecular dynamic (MD) simulations of RNA-binding structure and RNA-free structure have been performed. The simulation results show that an important helix α6 interacts with RNA in the "open" conformation, while helix α6 rotates toward the binding crevice and reduces the space of RNA-binding pocket in the "closed" conformation; it appears that helix α6 would clash with RNA while NP is in a "closed" state. In addition, to characterize the role of residues involved in the binding of RNA, the MD simulations of the double-mutant (W164A/F176A) and the single-mutant (G243P) RNA-binding NP complexes have been performed. Our MD simulations and molecular mechanics-generalized born surface area (MM-GBSA) energy calculations exhibit that the three mutant residues increase the binding affinity. Furthermore, we infer that the defect of the replication and transcription of viral genome is possibly due to the change of structural integrity rather than the reduction of RNA-binding affinity.


Assuntos
Vírus Lassa/química , Simulação de Dinâmica Molecular , Nucleoproteínas/química , RNA Viral/química , Proteínas Virais/química , Algoritmos , Sítios de Ligação , Cristalografia por Raios X , Humanos , Ligação de Hidrogênio , Vírus Lassa/genética , Vírus Lassa/metabolismo , Mutação , Conformação de Ácido Nucleico , Nucleoproteínas/genética , Nucleoproteínas/metabolismo , Ligação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , RNA Viral/genética , RNA Viral/metabolismo , Termodinâmica , Proteínas Virais/genética , Proteínas Virais/metabolismo
15.
J Biomol Struct Dyn ; 33(5): 1067-81, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-24865469

RESUMO

Mcl-1 has emerged as a potential therapeutic target in the treatment of several malignancies. Peptides representing BH3 region of pro-apoptotic proteins have been shown to bind the hydrophobic cleft of anti-apoptotic Mcl-1 and this segment is responsible for modulating the apoptotic pathways in living cells. Understanding the molecular basis of protein-peptide interaction is required to develop potent inhibitors specific for Mcl-1. Molecular dynamics simulations were performed for Mcl-1 in complex with three different BH3 peptides derived from Mcl-1, Bax, and Bim. Accordingly, the calculated binding free energies using MM-PBSA method are obtained and comparison with the experimentally determined binding free energies is made. The interactions involving two conserved charged residues (Aspi, and Arg/Lysi-4) and three upstream conserved hydrophobic residues (Leui-5, Ile/Vali-2, and Glyi-1, respectively) of BH3 peptides play the important roles in the structural stability of the complexes. The calculated results exhibit that the interactions of Bim BH3 peptides to Mcl-1 is stronger than the complex with Bax 19BH3 peptides. The hydrophobic residues (position i - 9, i - 8 and i + 2) of BH3 peptides can be involved in their inhibitory specificity. The calculated results can be used for designing more effective MCL-1 inhibitors.


Assuntos
Proteínas Reguladoras de Apoptose/química , Proteínas de Membrana/química , Simulação de Dinâmica Molecular , Proteína de Sequência 1 de Leucemia de Células Mieloides/química , Peptídeos/química , Proteínas Proto-Oncogênicas/química , Proteína X Associada a bcl-2/química , Sequência de Aminoácidos , Proteínas Reguladoras de Apoptose/genética , Proteínas Reguladoras de Apoptose/metabolismo , Proteína 11 Semelhante a Bcl-2 , Ligação Competitiva , Humanos , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Dados de Sequência Molecular , Mutação , Proteína de Sequência 1 de Leucemia de Células Mieloides/genética , Proteína de Sequência 1 de Leucemia de Células Mieloides/metabolismo , Peptídeos/genética , Peptídeos/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína , Proteínas Proto-Oncogênicas/genética , Proteínas Proto-Oncogênicas/metabolismo , Termodinâmica , Proteína X Associada a bcl-2/genética , Proteína X Associada a bcl-2/metabolismo
16.
J Mol Model ; 20(2): 2122, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24526384

RESUMO

Residue Gly86 is considered as the highly conversed residue in the HIV-1 protease. In our work, the detailed binding free energies for the wild-type (WT) and mutated proteases binding to the TMC-114 are estimated to investigate the protein-inhibitor binding and drug resistance mechanism by molecule dynamic simulations and molecular mechanics Poisson Boltzmann surface area (MM-PBSA) method. The binding affinities between the mutants and inhibitor are different than that in the wild-type complex and the major resistance to Darunavir (DRV) of G86A and G86S originate from the electrostatic energy and entropy, respectively. Furthermore, free energy decomposition analysis for the WT and mutated complexes on the basis of per-residue indicates that the mutagenesis influences the energy contribution of the residue located at three regions: active site region (residue 24-32), the flap region, and the region around the mutated residue G86 (residue 79-88), especially the flap region. Finally, further hydrogen bonds and structure analysis are carried out to detect the relationship between the energy and conformation. In all, the G86 mutations change the flap region's conformation. The experimental results are in good agreement with available results.


Assuntos
Metabolismo Energético , Protease de HIV/química , Simulação de Dinâmica Molecular , Sulfonamidas/química , Sítios de Ligação , Domínio Catalítico/genética , Darunavir , Resistência a Medicamentos/genética , Entropia , Protease de HIV/metabolismo , Humanos , Ligação de Hidrogênio , Complexos Multiproteicos/química , Complexos Multiproteicos/genética , Complexos Multiproteicos/metabolismo , Mutação , Ligação Proteica , Conformação Proteica , Sulfonamidas/metabolismo , Termodinâmica
17.
J Biomol Struct Dyn ; 31(3): 299-315, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22871039

RESUMO

Lassa virus can cause dreadful human hemorrhagic disease, for which there is no effective therapy. A recent study points out that the amino (N)-terminal domain of Lassa virus nucleoprotein (NP) plays an important role in viral RNA synthesis and firstly solved the X-ray crystal structures of NP complexed with the capped Deoxythymidine triphosphate (dTTP) analog, but the binding mode of m7GpppG to the N domain of NP, which is required for viral RNA transcription, has not been studied. In this study, molecular dynamics (MD) simulations have been carried out to investigate the characters of dTTP binding to two forms of NP, i.e. the NP without the C domain and the full-length NP model, using two different force fields, ff03 and ff99SB, respectively. Our calculated results show that the truncated model is reasonable and can replace the full protein model in the following MD simulations, and that ff99SB combined with the general AMBER force field is more suitable for sampling the structure of small molecule NP complex. From the comparisons of stability of hydrogen bonds between small molecule and protein in the dTTP and Uridine 5'-Triphosphate complexes, one finds that the stable hydrogen bonds between the second phosphate group of small molecules and two residues, Thr178 and Arg323, are critical for cap analogs binding to the N domain of NP. Additionally, docking method combined with MD simulations have been applied to predict the binding mode of m7GpppG to NP; and the hydrogen bond analysis and the binding free energy decomposition method (MM/GBSA) are conducted to study the interactions in the putative binding mode. The calculated results are expected to provide guidance for drug development.


Assuntos
Fosfatos de Dinucleosídeos/metabolismo , Vírus Lassa/metabolismo , Simulação de Dinâmica Molecular , Nucleoproteínas/metabolismo , Nucleotídeos de Timina/metabolismo , Aminoácidos/metabolismo , Fosfatos de Dinucleosídeos/química , Humanos , Ligação de Hidrogênio , Nucleoproteínas/química , Ligação Proteica , Termodinâmica , Timina/metabolismo , Nucleotídeos de Timina/química
18.
J Mol Model ; 19(2): 905-17, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23086459

RESUMO

BMS-488043, like its predecessor BMS-378806, is a small molecule that can block the interactions between gp120 and CD4, and has shown good clinical efficacy. However, the crystal structure of drug-gp120 complexes or the full-length gp120 free of bound ligand is unpublished until now. Docking combined with molecular dynamics simulation is used to investigate the binding mode between BMS-488043 and gp120. On the basis of the analysis of the simulated results, the plausible binding mode is acquired, such as the changes of binding mode in the trajectory and the calculated binding free energy. Subsequently, a number of residues which make contacts with the small molecule are studied by binding free energy decomposition to understand the mutation experiments, such as Trp427, Ser375, and Thr257 residues with the help of the acquired binding mode above. Especially, the importance of the hydrophobic groove formed by residues Ile371 and Gly472 which bind BMS-488043 is elaborated, which has not been explored much. In addition, theoretical investigations on the dynamics behavior of the gp120 associated with BMS-488043 enhanced binding are performed; the results indicate that the BMS-488043 may be more deeply inserted into the Phe43 cavity compared with the previous binding mode acquired by docking.


Assuntos
Aminoácidos/química , Proteína gp120 do Envelope de HIV/química , Inibidores da Fusão de HIV/química , HIV-1/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Piperazinas/química , Substituição de Aminoácidos , Sítios de Ligação , Humanos , Interações Hidrofóbicas e Hidrofílicas , Indóis , Cinética , Ligação Proteica , Ácido Pirúvico , Termodinâmica
19.
J Phys Chem B ; 116(34): 10219-33, 2012 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-22857012

RESUMO

Soluble epoxide hydrolase (sEH) has become a new therapeutic target for treating a variety of human diseases. The inhibition of human sEH hydrolase activity was studied by molecular docking and molecular dynamics (MD) simulation techniques. A set of six benzoxazole-based amide inhibitors binding to sEH has been studied through molecular docking, MD simulation, free energy calculations, and energy decomposition analysis. On the basis of molecular mechanics-generalized Born/surface area (MM-GB/SA) computation and normal-mode analysis (NMA), the obtained results indicate that the rank of calculated binding free energies (ΔΔGTOT) of these inhibitors is in excellent agreement with that of experimental bioactivity data (IC50). The correlation coefficient (r(2)) between the predicted ΔΔGTOT and IC50 is 0.88. van der Waals energies are the largest component of the total energies, and the entropy changes play an indispensable role in determining the ΔΔGTOT. Rational binding modes were discussed and determined by the docking results and binding free energies. The free energy decomposition of each residue reveals that the residue Trp334 dominates the most binding free energies among all residues and that the activities for these molecules to the sEH are not decided by hydrogen bonds or a certain residue but by the common effect of multiple side chains in the active site.


Assuntos
Amidas/farmacologia , Benzoxazóis/química , Inibidores Enzimáticos/farmacologia , Epóxido Hidrolases/antagonistas & inibidores , Amidas/química , Sítios de Ligação/efeitos dos fármacos , Inibidores Enzimáticos/química , Epóxido Hidrolases/química , Epóxido Hidrolases/metabolismo , Ligantes , Modelos Moleculares , Solubilidade , Relação Estrutura-Atividade
20.
J Mol Model ; 18(5): 1841-54, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-21850570

RESUMO

The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap region (residues 38-58) and the active site region (residues 23-32) in HIV-1 protease contribute 63.72% of the protease to the binding of the inhibitor. In particular, the mechanisms for the interactions of key residues of these species are fully explored and analyzed. Interestingly, the regression analyses show that both CAS and BFED based on the generalized Born model yield similar results, with a correlation coefficient of 0.94. However, compared to CAS, BFED is faster and can decompose the per-residue binding free-energy contributions into backbone and side-chain contributions. The results obtained in this study are useful for studying the binding mechanism between receptor and ligand and for designing potent inhibitors that can combat diseases.


Assuntos
Inibidores da Protease de HIV/química , Protease de HIV/química , HIV-1/química , Simulação de Dinâmica Molecular , Sulfonamidas/química , Uretana/análogos & derivados , Alanina/química , Domínio Catalítico , HIV-1/enzimologia , Cinética , Ligação Proteica , Termodinâmica , Uretana/química
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