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1.
J Chem Phys ; 151(8): 085101, 2019 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-31470695

RESUMO

Periodic molecular dynamics simulations of proteins may suffer from image interactions. Similarly, the hydrophobic effect required to keep a protein folded may not be enforced by small simulation cells. Accordingly, errors may arise both from the water concentration per se and the image interactions. Intrinsically disordered proteins are particularly sensitive, providing a worst-case estimate of the errors. Following this reasoning, we studied Aß40 (Aß), a disordered peptide central to Alzheimer's disease, by 100 different simulations with variable cell size from very large (20 Å) to very small (3 Å). Even for this very disordered peptide, most properties are not cell-size dependent, justifying the common use of modest-sized (10 Å) cells for simulating proteins. The radius of gyration, secondary structure, intrapeptide, and peptide-water hydrogen bonds are similar relative to standard deviations at any cell size. However, hydrophobic surface area increases significantly in small cells (confidence 95%, two-tailed t-test), as does the standard deviation in exposure and backbone conformations (>40% and >27%). Similar results were obtained for the force fields OPLS3e, Ambersb99-ILDN, and Charmm22*. The similar prevalence of structures and α-ß transitions in long and short simulations indicate small diffusion barriers, which we suggest is a defining hallmark of intrinsically disordered proteins. Whereas hydrophilic exposure dominates in large cells, hydrophobic exposure dominates in small cells, suggesting a weakening of the hydrophobic effect by image interactions and the few water layers available to keep the protein compact, with a critical limit of 2-3 water layers required to enforce the hydrophobic effect.


Assuntos
Peptídeos beta-Amiloides/química , Tamanho Celular , Proteínas Intrinsicamente Desordenadas/química , Simulação de Dinâmica Molecular , Humanos , Interações Hidrofóbicas e Hidrofílicas , Conformação Proteica
2.
J Chem Phys ; 151(8): 085102, 2019 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-31470725

RESUMO

In recent years, there has been a growing interest to quantify the energy landscape that governs ribosome dynamics. However, in order to quantitatively integrate theoretical predictions and experimental measurements, it is essential that one has a detailed understanding of the associated diffusive properties. Here, all-atom explicit-solvent simulations (50 µs of aggregate sampling) predict that the diffusion coefficient of a tRNA molecule will depend on its position within the ribosome. Specifically, during aa-tRNA accommodation (i.e., the process by which tRNA enters the ribosome), the apparent diffusion coefficient decreases by approximately an order of magnitude. By comparing these to values obtained with an energetically "smooth" model, we show that the observed nonuniform behavior likely arises from electrostatic and solvation interactions between the tRNA and ribosome. These calculations also reveal the hierarchical character of ribosomal energetics, where steric interactions induce a large-scale free-energy barrier, and short-scale roughness determines the rate of diffusive movement across the landscape.


Assuntos
Difusão , RNA de Transferência/metabolismo , Ribossomos/química , Ribossomos/metabolismo , Entropia , Simulação de Dinâmica Molecular , RNA de Transferência/química
3.
Phys Chem Chem Phys ; 21(37): 20678-20692, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31508628

RESUMO

In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory. The sampling is only performed in the phase space of the initial protein. We analyze the robustness of the method by comparing different approximations for the effective potential, the sampling of mutant residue geometries and observing the impact in the prediction of both bathocromic and hypsochromic shifts. As a test subject, we consider a red fluorescent protein variant with potential biotechnological applications.


Assuntos
Testes Genéticos/métodos , Luz , Proteínas/química , Proteínas/genética , Análise Espectral , Raios Ultravioleta , Simulação de Dinâmica Molecular , Mutação
4.
Phys Chem Chem Phys ; 21(37): 20750-20756, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31513191

RESUMO

"Intelligent" materials based on synthetic small molecules that become functional only under specific conditions provide new opportunities for developing regulated systems aimed at a large number of applications. For instance, biologically active supramolecular entities that are sensitive to environmental conditions, such as the presence of bacterial membranes, are extremely interesting in biomedicine. In this work, we have designed and investigated, using molecular dynamics simulations, a doubly modulable nanotube formed by the self-assembly of cyclic peptides sensitive to both the presence of a lipid membrane and the pH of the aqueous media. The cyclic peptides were designed to self-assemble into peptide nanotubes in the presence of a lipid bilayer and at low pH values. Under these conditions, the residual side chains point outside the cyclic peptides, being exposed to the lipid bilayer, and the inner groups (carboxylic acids) are protonated, thus allowing the permeation of water and preventing that of ions. Higher pH values are expected to create carboxylate groups at the lumen of the peptides, leading to the disassembly of the nanotube, the attraction and translocation of ions towards the hydrophobic core of the bilayer, and eventually killing the target malignant cells. Our results suggest that by introducing a second switch in a membrane sensitive system, it is possible to modulate its interaction with the lipid bilayer. This opens the door to new strategies for the preparation of antimicrobial peptides that interact at the membrane level.


Assuntos
Nanotubos de Peptídeos/química , Peptídeos Cíclicos/química , Anti-Infecciosos/química , Bactérias/química , Concentração de Íons de Hidrogênio , Bicamadas Lipídicas/química , Simulação de Dinâmica Molecular
5.
Phys Chem Chem Phys ; 21(37): 20606-20612, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31528919

RESUMO

In this work, the interaction between an Auramine O (AuO) fluorescent molecular rotor and natural DNA, its thermodynamic aspects and the resulting variation of the optical properties upon binding are addressed by a combined spectroscopic (UV-vis and fluorescence) and computational approach. DNA binding causes a shift in the maximum of absorption from 432 nm to 444 nm, a decrease of the extinction coefficient and a dramatic enhancement of fluorescence emission, these results being in agreement with intercalation into the polynucleotide helix. Intercalation is indeed confirmed by the thermodynamic parameters for the binding reaction (in particular, the highly negative ΔH). Theoretical modelling at the TD-DFT level was done on a simplified model system consisting of the AuO molecule intercalated between two DNA base pairs. The evolution of the calculated vertical transitions quantitatively reproduces the experimentally observed hypo- and bathochromic shifts, thus confirming the intercalation hypothesis.


Assuntos
Benzofenoneídio/química , DNA/química , Modelos Químicos , Análise Espectral , Fluorescência , Simulação de Dinâmica Molecular
6.
Phys Chem Chem Phys ; 21(37): 21038-21048, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31528920

RESUMO

Dramatically different properties have been observed for two types of osmolytes, i.e., trimethylamine N-oxide (TMAO) and urea, in a protein folding process. Great progress has been made in revealing the potential underlying mechanism of these two osmolyte systems. However, many problems still remain unsolved. In this paper, we propose to use the persistent homology to systematically study the osmolytes' molecular aggregation and their hydrogen-bonding network from a global topological perspective. It has been found that, for the first time, TMAO and urea show two extremely different topological behaviors, i.e., an extensive network and local clusters, respectively. In general, TMAO forms highly consistent large loop or circle structures in high concentrations. In contrast, urea is more tightly aggregated locally. Moreover, the resulting hydrogen-bonding networks also demonstrate distinguishable features. With a concentration increase, TMAO hydrogen-bonding networks vary greatly in their total number of loop structures and large-sized loop structures consistently increase. In contrast, urea hydrogen-bonding networks remain relatively stable with slight reduction of the total loop number. Moreover, the persistent entropy (PE) is, for the first time, used in characterization of the topological information of the aggregation and hydrogen-bonding networks. The average PE systematically increases with the concentration for both TMAO and urea, and decreases in their hydrogen-bonding networks. But their PE variances have totally different behaviors. Finally, topological features of the hydrogen-bonding networks are found to be highly consistent with those from the ion aggregation systems, indicating that our topological invariants can characterize intrinsic features of the "structure making" and "structure breaking" systems.


Assuntos
Metilaminas/química , Ureia/química , Entropia , Hidrogênio/química , Ligações de Hidrogênio , Simulação de Dinâmica Molecular , Agregação Patológica de Proteínas , Homologia Estrutural de Proteína
7.
Gene ; 720: 144082, 2019 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-31476406

RESUMO

The enzyme ß-Ketoacyl ACP synthase I (KasA) is a potent drug target in mycolic acid pathway of Mycobacterium tuberculosis (Mtb). In the present study, we investigated the structural dynamics of wild-type (WT) and mutants KasA (D66N, G269S, G312S, and F413L) in both monomer and dimer form to provide insight into protein structural stability. To gain better understanding of structural flexibility of KasA, combined molecular dynamics and essential dynamics were employed to analyze the conformational changes induced by non-active site mutations. The results confirm that non-active site mutations lower the structural stability in dimer KasA as compared to WT. The protein network topology and close residue interactions of WT and mutant residues of KasA have been predicted through residue interaction network analysis (RIN). Non-active site mutations distort RIN architecture and subsequently affect the drug binding landscape. T-pad associated with mode vector analysis comprehensively pronounces the structural impact caused by non-active site mutations. It also identified the critical fluctuating residues present in the gate segment (GS) region (115-147). The non-active site mutations altered the structural stability of the mutant protein structures, and these mutations may be a cause for the resistance mechanism of KasA against anti-tuberculosis drugs. Further, it is observed that dimer mutant KasA proteins display much more structural flexibility than WT at the ligand binding site which is evident from the binding site analysis and hydrogen bond interaction patterns. This study provides a better understanding of the structural dynamic behaviour of KasA mutants, thereby facilitating the need to find a novel and potent inhibitor against Mtb.


Assuntos
3-Oxoacil-(Proteína de Transporte de Acila) Sintase/química , Proteínas de Bactérias/química , Isoenzimas/química , Proteínas Mutantes/química , Mutação , Mycobacterium tuberculosis/enzimologia , Tuberculose/microbiologia , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/genética , Proteínas de Bactérias/genética , Isoenzimas/genética , Simulação de Dinâmica Molecular , Proteínas Mutantes/genética , Conformação Proteica , Tuberculose/genética , Tuberculose/metabolismo
8.
J Chem Phys ; 151(7): 074109, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31438708

RESUMO

It is a challenge to obtain an accurate model of the state-to-state dynamics of a complex biological system from molecular dynamics (MD) simulations. In recent years, Markov state models have gained immense popularity for computing state-to-state dynamics from a pool of short MD simulations. However, the assumption that the underlying dynamics on the reduced space is Markovian induces a systematic bias in the model, especially in biomolecular systems with complicated energy landscapes. To address this problem, we have devised a new approach we call quasistationary distribution kinetic Monte Carlo (QSD-KMC) that gives accurate long time state-to-state evolution while retaining the entire time resolution even when the dynamics is highly non-Markovian. The proposed method is a kinetic Monte Carlo approach that takes advantage of two concepts: (i) the quasistationary distribution, the distribution that results when a trajectory remains in one state for a long time (the dephasing time), such that the next escape is Markovian, and (ii) dynamical corrections theory, which properly accounts for the correlated events that occur as a trajectory passes from state to state before it settles again. In practice, this is achieved by specifying, for each escape, the intermediate states and the final state that has resulted from the escape. Implementation of QSD-KMC imposes stricter requirements on the lengths of the trajectories than in a Markov state model approach as the trajectories must be long enough to dephase. However, the QSD-KMC model produces state-to-state trajectories that are statistically indistinguishable from an MD trajectory mapped onto the discrete set of states for an arbitrary choice of state decomposition. Furthermore, the aforementioned concepts can be used to construct a Monte Carlo approach to optimize the state boundaries regardless of the initial choice of states. We demonstrate the QSD-KMC method on two one-dimensional model systems, one of which is a driven nonequilibrium system, and on two well-characterized biomolecular systems.


Assuntos
Simulação de Dinâmica Molecular , Método de Monte Carlo , Cinética
9.
Phys Chem Chem Phys ; 21(32): 17821-17835, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31373340

RESUMO

The rise of New Delhi metallo-beta-lactamase-1 (NDM-1) producers is a major public health concern due to carbapenem resistance. Infections caused by carbapenem-resistant enterobacteria (CRE) are classified as a serious problem. To understand the structure and function of NDM-1, an amino acid replacement approach is considered as one of the methods to get structural insight. Therefore, we have generated novel mutations (N193A, S217A, G219A and T262A) near active sites and an omega-like loop to study the role of conserved residues of NDM-1. The minimum inhibitory concentrations (MICs) of ampicillin, imipenem, meropenem, cefotaxime, cefoxitin and ceftazidime for all mutants were found to be reduced 2 to 6 fold, compared to a wild type NDM-1 producing strain. The Km values increased while Kcat and Kcat/Km values were decreased compared to wild type. The affinity as well as the catalysis properties of these mutants were reduced considerably for imipenem, meropenem, cefotaxime, cefoxitin, and ceftazidimem compared to wild type, hence the catalytic efficiencies (Kcat/Km) of all mutant enzymes were reduced owing to the poor affinity of the enzyme. The IC50 values of these mutants with respect to each drug were reduced compared to wild type NDM-1. MD simulations and docking results from the mutant protein models, along with the wild type example, showed stable and consistent RMSD, RMSF and Rg behavior. The α-helix content values of all mutant proteins were reduced by 13%, 6%, 14% and 9% compared to NDM-1. Hence, this study revealed the impact role of active sites near residues on the enzyme catalytic activity of NDM-1.


Assuntos
Antibacterianos/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , beta-Lactamases/química , Antibacterianos/farmacologia , Biocatálise , Domínio Catalítico , Farmacorresistência Bacteriana , Cinética , Testes de Sensibilidade Microbiana , Mutagênese Sítio-Dirigida , Mutação , Ligação Proteica , Estrutura Secundária de Proteína , Termodinâmica , beta-Lactamases/genética , beta-Lactamases/metabolismo
10.
Dokl Biochem Biophys ; 486(1): 220-223, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31367826

RESUMO

Cardiolipin (CL) plays a central role in lipid peroxidation (LPO) of the mitochondrial inner membrane due to higher content of unsaturated fatty acids in CL in comparison with the other phospholipids. CL oxidation plays an important role in the regulation of various intracellular signaling pathways and its excessive oxidation contributes to the development of various pathologies and, possibly, participates in the aging process. Mitochondria-targeted antioxidants containing triphenylphosphonium (TPP+) effectively protect CL from oxidation. It is assumed that fluorescent probes on the basis of the C11-BODIPY fluorophore sensitive to LPO and containing TPP+ can selectively register CL oxidation. To test this possibility, we carried out a molecular dynamic simulation of such probes in a model mitochondrial membrane. It is shown that the probes are located in the membrane at the same depth as the unsaturated bonds in CL molecules sensitive to oxidation. Increasing the length of the linker that binds the fluorophore and TPP+ residue ha little effect on the position of the probe in the membrane. This indicates the possibility of modifying the linker to increase the selectivity of the probes to CL.


Assuntos
Corantes Fluorescentes/metabolismo , Peroxidação de Lipídeos , Membranas Mitocondriais/metabolismo , Simulação de Dinâmica Molecular , Compostos de Boro/metabolismo
11.
J Chem Theory Comput ; 15(9): 5046-5057, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31390517

RESUMO

Halogenated BODIPY derivatives are emerging as important candidates for photodynamic therapy of cancer cells due to their high triplet quantum yield. We probed fundamental photophysical properties and interactions with biological environments of such photosensitizers. To this end, we employed static TD-DFT quantum chemical calculations as well as TD-DFT surface hopping molecular dynamics on potential energy surfaces resulting from the eigenstates of the total electronic Hamiltonian including the spin-orbit (SO) coupling. Matrix elements of an effective one-electron spin-orbit Hamiltonian between singlet and triplet configuration interaction singles (CIS) auxiliary wave functions are calculated using a new code capable of dealing with singlets and both restricted and unrestricted triplets built up from up to three different and independent sets of (singlet, alpha, and beta) molecular orbitals. The interaction with a biological environment was addressed by using classical molecular dynamics (MD) in a scheme that implicitly accounts for electronically excited states. For the surface hopping trajectories, an accelerated MD approach was used, in which the SO couplings are scaled up, to make the calculations computationally feasible, and the lifetimes are extrapolated back to unscaled SO couplings. The lifetime of the first excited singlet state estimated by semiclassical surface hopping simulations is 139 ± 75 ps. Classical MD demonstrates that halogenated BODIPY in the ground state, in contrast to the unsubstituted one, is stable in the headgroup region of minimalistic cell membrane models, and while in the triplet state, the molecule relocates to the membrane interior ready for further steps of photodynamic therapy.


Assuntos
Compostos de Boro/química , Simulação de Dinâmica Molecular , Fotoquimioterapia , Teoria da Densidade Funcional , Processos Fotoquímicos , Fármacos Fotossensibilizantes/química , Teoria Quântica , Propriedades de Superfície
12.
J Chem Theory Comput ; 15(9): 5103-5115, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31402649

RESUMO

Intrinsically disordered proteins (IDPs) play key roles in biology and disease, rationalizing the wide interest in deriving accurate solution ensembles of IDPs. Molecular dynamics (MD) simulations of IDPs often suffer from force-field inaccuracies, suggesting that simulations must be complemented by experimental data to obtain physically correct ensembles. We present a method for integrating small-angle X-ray scattering (SAXS) data on-the-fly into MD simulations of disordered systems, with the aim to bias the conformational sampling toward agreement with ensemble-averaged SAXS data. By coupling a set of parallel replicas to the data and following the principle of maximum entropy, this method applies only a minimal bias. Using the RS peptide as a test case, we analyze the influence of (i) the number of parallel replicas, (ii) the scaling of the force constant for the SAXS-derived biasing energy with the number of parallel replicas, and (iii) the force field. The refined ensembles are cross-validated against experimental 3JHN-Hα couplings and further compared in terms of Cα distance maps and secondary structure content. Remarkably, we find that the applied force field only has a small influence on the SAXS-refined ensemble, suggesting that incorporating SAXS data into MD simulations may greatly reduce the force-field bias.


Assuntos
Entropia , Proteínas Intrinsicamente Desordenadas/química , Simulação de Dinâmica Molecular , Espalhamento a Baixo Ângulo , Difração de Raios X , Conformação Proteica
13.
J Chem Theory Comput ; 15(9): 4974-4981, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31402652

RESUMO

Predicting the costructure of small-molecule ligands and their respective target proteins has been a long-standing problem in drug discovery. For weak binding compounds typically identified in fragment-based screening (FBS) campaigns, determination of the correct binding site and correct binding mode is usually done experimentally via X-ray crystallography. For many targets of pharmaceutical interest, however, establishing an X-ray system which allows for sufficient throughput to support a drug discovery project is not possible. In this case, exploration of fragment hits becomes a very laborious and consequently slow process with the generation of protein/ligand cocrystal structures as the bottleneck of the entire process. In this work, we introduce a computational method which is able to reliably predict binding sites and binding modes of fragment-like small molecules using solely the structure of the apoprotein and the ligand's chemical structure as input information. The method is based on molecular dynamics simulations and Markov-state models and can be run as a fully automated protocol requiring minimal human intervention. We describe the application of the method to a representative subset of different target classes and fragments from historical FBS efforts at Boehringer Ingelheim and discuss its potential integration into the overall fragment-based drug discovery workflow.


Assuntos
Cadeias de Markov , Simulação de Dinâmica Molecular , Proteínas/química , Sítios de Ligação , Cristalografia por Raios X , Humanos , Ligantes
14.
J Chem Theory Comput ; 15(9): 4982-5000, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31411469

RESUMO

In this work, we report the development of Drude polarizable force field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of the existing Drude polarizable carbohydrate force field. The force field parameters have been developed in a hierarchical manner, reproducing the quantum mechanical gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for carboxylate and N-acetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from nuclear magnetic resonance experiments. The parameter development resulted in the incorporation of d-glucuronate, l-iduronate, N-acetyl-d-glucosamine (GlcNAc), and N-acetyl-d-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of d-glucuronate and N-acetyl-d-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations, it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan, resulting in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.


Assuntos
Aminas/química , Carboidratos/química , Simulação de Dinâmica Molecular , Teoria Quântica , Eletricidade Estática
15.
J Chem Theory Comput ; 15(9): 5144-5153, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31411882

RESUMO

Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is an enhanced conformational sampling method of proteins, which does not rely on knowledge of the target structure. It makes use of cyclic resampling from some relevant initial structures to expand the searched conformational subspace. The efficiency of nt-PaCS-MD depends on the selections of these initial structures. They are usually stochastically occurring perturbed structures at which larger conformation transitions are about to happen. Reliable identification of these is the key to using nt-PaCS-MD. Two new parameters, the moving root-mean-square deviation (mRMSD) and the inner products of the backbone dihedral angles Φ and Ψ, are introduced as indicators of conformational outliers in MD trajectories. Both are based on the analysis of a time-localized set of coordinates, overcoming the need for a target structure while still capturing the complexity of the conformational transition. The reference to which the mRMSD relates is the close surrounding of the i-th conformation, often the (i-1)st one. Hence the name "time-localized" analysis. In this work, we focus on its interplay with nt-PaCS-MD and show that it increases its effectiveness compared to older versions. The target system is the midsized protein T4 lysozyme (in explicit water) on which we demonstrate the open-closed transition without referring to any target configuration. Additionally, we show that the short MD trajectories can be used for the construction of a free energy landscape of the conformational transition based on the Markov state model.


Assuntos
Simulação de Dinâmica Molecular , Muramidase/química , Bacteriófago T4/enzimologia , Muramidase/metabolismo , Conformação Proteica , Fatores de Tempo
16.
J Agric Food Chem ; 67(37): 10412-10422, 2019 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-31464443

RESUMO

In this study, aggregation of fucoxanthin (FX) and its effects on binding and delivery properties of whey proteins were explored. Initially, the H- and J-aggregates of FX were successfully prepared by adjusting the water/ethanol ratio and water-dripping rate. The transition from J- to H-aggregates was observed over the standing time. Then, the molecular arrangement of FX H-aggregates was analyzed using the point-dipole approximation model and molecular dynamics, showing that their intermolecular distance and angle were about 5.0-6.7 Å and -35° to 35°, respectively. The transformation of J- to H-aggregates was also observed during molecular dynamics, with a shortened intermolecular distance, a reduced solvent accessible surface area, an enhanced interaction force, and a narrowed dihedral angle. Further, the interactions of whey proteins with different forms of FX were investigated, indicating that both ß-lactoglobulin and whey protein isolates could form complexes with the monomers, H-aggregates, and J-aggregates of FX. In terms of affinity, whey proteins bound FX monomers more strongly than aggregates. Furthermore, the complexes comprising whey proteins and monomeric FX had better delivery capabilities than aggregated FX, manifested in encapsulation efficiency, physical stability, and bioaccessibility.


Assuntos
Proteínas do Soro do Leite/química , Xantofilas/química , Concentração de Íons de Hidrogênio , Lactoglobulinas/química , Simulação de Dinâmica Molecular , Agregados Proteicos , Ligação Proteica
17.
J Phys Chem A ; 123(36): 7710-7719, 2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31433182

RESUMO

Maleamate amidohydrolase (NicF) is a key enzyme in vitamin B3 metabolism that catalyzes the hydrolysis of maleamate to produce maleic acid and ammonia. Unlike most members from the amidohydrolase superfamily it does not require a metal ion. Here, we use multiscale computational enzymology to investigate the catalytic mechanism, substrate binding, oxyanion hole, and roles of key active site residues of NicF from Bordetella bronchiseptica. In particular, molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) and QTAIM methods have been applied. The mechanism of the NicF-catalyzed reaction proceeds by a nucleophilic addition-elimination sequence involving the formation of a thioester enzyme intermediate (IC2 in stage 1) followed by hydrolysis of the thioester bond to form the products (stage 2). Consequently, the formation of IC2 in stage 1 is the rate-limiting step with a barrier of 88.8 kJ·mol-1 relative to the reactant complex, RC. Comparisons with related metal-dependent enzymes, particularly the zinc-dependent nicotinamidase from Streptococcus pneumonia (SpNic), have also been made to further illustrate unique features of the present mechanism. Along with -NH- donor groups of the oxyanion hole (i.e., HN-Thr146, HN-Cys150), the active site ß-hydroxyl of threonine (HO-ßThr146) is concluded to play a role in stabilizing the carbonyl oxygen of maleamate during the mechanism.


Assuntos
Amidoidrolases/química , Amidoidrolases/metabolismo , Biocatálise , Maleatos/metabolismo , Simulação de Dinâmica Molecular , Teoria Quântica , Bordetella bronchiseptica/enzimologia , Hidrólise , Maleatos/química , Estrutura Molecular
18.
Phys Chem Chem Phys ; 21(35): 19298-19310, 2019 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-31451813

RESUMO

The ice/water interface recognition mechanism of antifreeze proteins (AFPs) is highly contentious. Conventionally, protein adsorption on a solid surface is primarily driven by the polar interactions between the hydrophilic residues of the protein and interfacial water of the solid surface. Ice surface recognition by a type III AFP is surprising in this context where the ice binding surface (IBS) is hydrophobic. The present study provides molecular insight into the unusual interface recognition phenomenon of a type III AFP (QAE isoform) from Macrozoarces americanus. Potential of mean force calculations show that the type III AFP adsorbs on the ice surface mediated through a layer of ordered water. Molecular dynamics simulations at lower than ambient temperature reveal that the flat hydrophobic IBS induces ordering of water. The excellent geometrical synergy between the hydration water structure around the IBS and water arrangements on the pyramidal surface favours adsorption on the pyramidal plane. Mutations that interrupt the hydration shell water ordering essentially lead to less efficient adsorption, which greatly reduces the anti-freezing activity of the AFP. Binding free energy calculations of the wild-type and several mutant AFPs reveal that the binding affinity is linearly correlated with the experimentally observed thermal hysteresis activity. Therefore, binding to a specific ice plane with considerable affinity is the dictating factor of the anti-freeze activity for a type III AFP. Mechanistic insights into the ice binding process of the wild-type and different mutant AFPs obtained from this study pave the way for rational design of type III variants with much improved activity, which possesses ample industrial applicability, particularly in cryo-preservation.


Assuntos
Proteínas Anticongelantes/química , Proteínas de Peixes/química , Gelo , Perciformes , Água/química , Animais , Proteínas Anticongelantes/genética , Temperatura Baixa , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Simulação de Dinâmica Molecular , Mutação , Ligação Proteica
19.
Phys Chem Chem Phys ; 21(35): 18958-18969, 2019 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-31453590

RESUMO

Enhanced sampling has been extensively used to capture the conformational transitions in protein folding, but it attracts much less attention in the studies of protein-protein recognition. In this study, we evaluated the impact of enhanced sampling methods and solute dielectric constants on the overall accuracy of the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics/generalized Born surface area (MM/GBSA) approaches for the protein-protein binding free energy calculations. Here, two widely used enhanced sampling methods, including aMD and GaMD, and conventional molecular dynamics (cMD) simulations with two AMBER force fields (ff03 and ff14SB) were used to sample the conformations for 21 protein-protein complexes. The MM/PBSA and MM/GBSA calculation results illustrate that the standard MM/GBSA based on the cMD simulations yields the best Pearson correlation (rp = -0.523) between the predicted binding affinities and the experimental data, which is much higher than that given by MM/PBSA (rp = -0.212). Two enhanced sampling methods (aMD and GaMD) are indeed more efficient for conformational sampling, but they did not improve the binding affinity predictions for protein-protein systems, suggesting that the aMD or GaMD sampling (at least in short timescale simulations) may not be a good choice for the MM/PBSA and MM/GBSA predictions of protein-protein complexes. The solute dielectric constant of 1.0 is recommended to MM/GBSA, but a higher solute dielectric constant is recommended to MM/PBSA, especially for the systems with higher polarity on the protein-protein binding interfaces. Then, a preliminary assessment of the MM/GBSA calculations based on a variable dielectric generalized Born (VDGB) model was conducted. The results highlight the potential power of VDGB in the free energy predictions for protein-protein systems, but more thorough studies should be done in the future.


Assuntos
Técnicas de Química Analítica/métodos , Modelos Químicos , Proteínas/química , Técnicas de Química Analítica/normas , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica , Reprodutibilidade dos Testes
20.
Phys Chem Chem Phys ; 21(35): 19327-19341, 2019 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-31453592

RESUMO

The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted.


Assuntos
Dano ao DNA , Lipídeos de Membrana/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Colesterol/química , Lipídeos de Membrana/química , Simulação de Dinâmica Molecular , Fosfolipídeos/química , Espécies Reativas de Nitrogênio/sangue , Espécies Reativas de Nitrogênio/metabolismo , Espécies Reativas de Oxigênio/sangue , Vesículas Transportadoras/química
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