共查询到20条相似文献，搜索用时 15 毫秒
1.
Moutiez M Burova TV Haertlé T Quéméneur E 《Protein science : a publication of the Protein Society》1999,8(1):106-112
The mechanism of the disulfide-bond forming enzyme DsbA depends on the very low pKa of a cysteine residue in its active-site and on the relative instability of the oxidized enzyme compared to the reduced one. A thermodynamic cycle has been used to correlate its redox properties to the difference in the free energies of folding (deltadeltaGred/ox) of the oxidized and reduced forms. However, the relation was proved unsatisfied for a number of DsbA variants. In this study, we investigate the thermodynamic and redox properties of a highly destabilized variant DsbA(P151A) (substitution of cis-Pro151 by an alanine) by the means of intrinsic tryptophan fluorescence and by high-sensitivity differential scanning calorimetry (HS-DSC). When the value of deltadeltaGred/ox obtained fluorimetrically for DsbA(P151A) does not correlate with the value expected from its redox potential, the value of deltadeltaGred/ox provided by HS-DSC are in perfect agreement with the predicted thermodynamic cycle for both wild-type and variant. HS-DSC data indicate that oxidized wild-type enzyme and the reduced forms of both wild-type and variant unfold according to a two-state mechanism. Oxidized DsbA(P151A) shows a deviation from two-state behavior that implies the loss of interdomain cooperativity in DsbA caused by Pro151 substitution. The presence of chaotrope in fluorimetric measurements could facilitate domain uncoupling so that the fluorescence probe (Trp76) does not reflect the whole unfolding process of DsbA(P151A) anymore. Thus, theoretical thermodynamic cycle is respected when an appropriate method is applied to DsbA unfolding under conditions in which protein domains still conserve their cooperativity. 相似文献
2.
Morgan Lawrenz Jeff Wereszczynski Rommie Amaro Ross Walker Adrian Roitberg J. Andrew McCammon 《Proteins》2010,78(11):2523-2532
The highly pathogenic influenza strains H5N1 and H1N1 are currently treated with inhibitors of the viral surface protein neuraminidase (N1). Crystal structures of N1 indicate a conserved, high affinity calcium binding site located near the active site. The specific role of this calcium in the enzyme mechanism is unknown, though it has been shown to be important for enzymatic activity and thermostability. We report molecular dynamics (MD) simulations of calcium‐bound and calcium‐free N1 complexes with the inhibitor oseltamivir (marketed as the drug Tamiflu), independently using both the AMBER FF99SB and GROMOS96 force fields, to give structural insight into calcium stabilization of key framework residues. Y347, which demonstrates similar sampling patterns in the simulations of both force fields, is implicated as an important N1 residue that can “clamp” the ligand into a favorable binding pose. Free energy perturbation and thermodynamic integration calculations, using two different force fields, support the importance of Y347 and indicate a +3 to +5 kcal/mol change in the binding free energy of oseltamivir in the absence of calcium. With the important role of structure‐based drug design for neuraminidase inhibitors and the growing literature on emerging strains and subtypes, inclusion of this calcium for active site stability is particularly crucial for computational efforts such as homology modeling, virtual screening, and free energy methods. Proteins 2010. © 2010 Wiley‐Liss, Inc. 相似文献
3.
Yang Yu Igor D. Petrik Kelly N. Chacón Parisa Hosseinzadeh Honghui Chen Ninian J. Blackburn Yi Lu 《Protein science : a publication of the Protein Society》2017,26(2):218-226
Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, few report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or “rack‐induced” state for ET functions. We herein report circular permutation of azurin by linking the N‐ and C‐termini and creating new termini in the loops between 1st and 2nd β strands or between 3rd and 4th β strands. Characterization by electronic absorption, electron paramagnetic spectroscopies, as well as crystallography and cyclic voltammetry revealed that, while the overall structure and the primary coordination sphere of the circular permutated azurins remain the same as those of native azurin, their reduction potentials increased by 18 and 124 mV over that of WTAz. Such increases in reduction potentials can be attributed to subtle differences in the hydrogen‐bonding network in secondary coordination sphere around the T1Cu center. 相似文献
4.
Matthew C.F. Wander 《Molecular simulation》2013,39(5):335-340
While force-field development has been discussed extensively in the literature, the question of what analytical expressions make the best function choices, particularly in the context of matching quantum mechanic potential energy surfaces (PES), is less explored. Traditional forms based upon harmonic oscillators and Lennard-Jones types have dominated the field owing to the focus on fitting properties. However, with the advent of gradient-fitting approaches, it is now possible with the correct force-field expressions to achieve consistent high-accuracy results with molecular dynamics calculations. Using the general principle that power series can fit surfaces of any shape well, we have utilised harmonic series functions to fit a two-body PES represented by a Morse function. The harmonic functions are fast because they have only integer exponents, and they fit accurately with a limited number of terms. 相似文献
5.
Molecular interaction between p53 tumor suppressor and the copper protein azurin (AZ) has been demonstrated to enhance p53 stability and hence antitumoral function, opening new perspectives in cancer treatment. While some experimental work has provided evidence for AZ binding to p53, no crystal structure for the p53-AZ complex was solved thus far. In this work the association between AZ and the p53 DNA-binding domain (DBD) was investigated by computational methods. Using a combination of rigid-body protein docking, experimental mutagenesis information, and cluster analysis 10 main p53 DBD-AZ binding modes were generated. The resulting structures were further characterized by molecular dynamics (MD) simulations and free energy calculations. We found that the highest scored docking conformation for the p53 DBD-AZ complex also yielded the most favorable free energy value. This best three-dimensional model for the complex was validated by using a computational mutagenesis strategy. In this structure AZ binds to the flexible L(1) and s(7)-s(8) loops of the p53 DBD and stabilizes them through protein-protein tight packing interactions, resulting in high degree of both surface matching and electrostatic complementarity. 相似文献
6.
A coarse‐grained potential for protein simulations and fold ranking is presented. The potential is based on a two‐point model of individual amino acids and a specific implementation of hydrogen bonding. Parameters are determined for distance dependent pair interactions, pseudo bonds, angles, and torsions. A scaling factor for a hydrogen bonding term is also determined. Iterative sampling for 4867 proteins reproduces distributions of internal coordinates and distances observed in the Protein Data Bank. The adjustment of the potential and resampling are in the spirit of the generalized ensemble approach. No native structure information (e.g., secondary structure) is used in the calculation of the potential or in the simulation of a particular protein. The potential is subject to two tests as follows: (i) simulations of 956 globular proteins in the neighborhood of their native folds (these proteins were not used in the training set) and (ii) discrimination between native and decoy structures for 2470 proteins with 305,000 decoys and the “Decoys ‘R’ Us” dataset. In the first test, 58% of tested proteins stay within 5 Å from the native fold in Molecular Dynamics simulations of more than 20 nanoseconds using the new potential. The potential is also useful in differentiating between correct and approximate folds providing significant signal for structure prediction algorithms. Sampling with the potential consistently regenerates the distribution of distances and internal coordinates it learned. Nevertheless, during Molecular Dynamics simulations structures are found that reproduce the learned distributions but are far from the native fold. Proteins 2009. © 2009 Wiley‐Liss, Inc. 相似文献
7.
p53 is a human tumour suppressor which regulates multiple cellular processes, including cell growth, genomic stability and cell death. Recent works have demonstrated the bacterial redox protein azurin to enter cancer cells and induce apoptosis through p53 stabilization, resulting in a tumour growth regression. Azurin has been shown to bind p53 although many details of the complex formed by these two proteins are still poorly characterized. Here, we get insight into the kinetics of this complex formation, by exploring the interaction between p53 and azurin in their environment by single molecule force spectroscopy. To this aim, azurin has been linked to the atomic force microscope tip, whereas p53 has been immobilized onto a gold substrate. Therefore, by performing force-distance cycles we have detected specific recognition events between p53 and azurin, displaying unbinding forces of around 70 pN for an applied loading rate of 3 nN s(-1). The specificity of these events has been assessed by the significant reduction of their frequency observed after blocking the p53 sample by an azurin solution. Moreover, by measuring the rupture force as a function of the loading rate we have determined the dissociation rate constant of this complex to be approximately 0.1 s(-1). Our findings are here discussed in connection with results obtained in bulk experiments, with the aim of clarifying some molecular details of the p53-azurin complex that may help designing new anticancer strategy. 相似文献
8.
Molecular dynamics simulations were carried out to calculate the free energy change difference of two collagen-like peptide models for Gly --> Ser mutations causing two different osteogenesis imperfecta phenotypes. These simulations were performed to investigate the impact of local amino acid sequence environment adjacent to a mutation site on the stability of the collagen. The average free energy differences for a Gly --> Ser mutant relative to a wild type are 3.4 kcal/mol and 8.2 kcal/mol for a nonlethal site and a lethal site, respectively. The free energy change differences of mutant containing two Ser residues relative to the wild type at the nonlethal and lethal mutation sites are 4.6 and 9.8 kcal/mol, respectively. Although electrostatic interactions stabilize mutants containing one or two Ser residues at both mutation sites, van der Waals interactions are of sufficient magnitude to cause a net destabilization. The presence of Gln and Arg near the mutation site, which contain large and polar side chains, provide more destabilization than amino acids containing small and nonpolar side chains. 相似文献
9.
Mihaly Mezei 《Molecular simulation》2013,39(2-6):225-239
Abstract The free-energy simulation methodology is reviewed from the point of view of calculating large free-energy differences. The advantages of the nearly linear thermodynamic integration based on Gaussian quadrature are highlighted and its performance is characterized on systems ranging from the Lennard-Jones fluid to the A to B transition of DNA oligomers. A technique for optimizing the runlength at each quadrature point is given. Examples for the sensitivity of the calculated free energy to the atomic charges used are also presented. 相似文献
10.
11.
Gloria Funari Fabio Domenici Lavinia Nardinocchi Rosa Puca Gabriella D'Orazi Anna Rita Bizzarri Salvatore Cannistraro 《Journal of molecular recognition : JMR》2010,23(4):343-351
Azurin, a bacterial protein, can be internalized in cancer cells and induce apoptosis. Such anticancer effect is coupled to the formation of a complex with the tumour‐suppressor p53. The mechanism by which azurin stabilizes p53 and the binding sites of their complex are still under investigation. It is also known that the predominant mechanism for p53 down‐regulation implies its association to Mdm2, the main ubiquitin ligase affecting its stability. However, the p53/Mdm2 interaction, occurring at the level of both their N‐terminal domains, has been characterized so far by experiments involving only partial domains of these proteins. The relevance of the p53/Mdm2 complex as a possible target of the anticancer therapies requires a deeper study of this complex as made up of the two entire proteins. Moreover, the apparent antagonist action of azurin against Mdm2, with respect of p53 regulation, might suggest the possibility that azurin binds p53 at the same site of Mdm2, preventing in such a way p53 and Mdm2 from association and thus p53 from degradation. By following the interaction of the two entire proteins by atomic force spectroscopy, we have assessed the formation of a specific complex between p53 and Mdm2. We found for it a binding strength and a dissociation rate constant typical of dynamical protein–protein interactions and we observed that azurin, even if capable to bind p53, does not compete with Mdm2 for the same binding site on p53. The formation of the p53/Mdm2/azurin ternary complex might suggest an alternative anti‐cancer mechanism adopted by azurin. Copyright © 2009 John Wiley & Sons, Ltd. 相似文献
12.
Brent L. Lee 《Molecular simulation》2018,44(13-14):1147-1157
AbstractComputer simulations of passive membrane permeation provide important microscopic insights into the molecular mechanism of this important biological process that are complementary to experimental data. Our review focuses on the main approaches for calculating the free energy, or potential of mean force, for permeation of small molecules through lipid bilayers. The theoretical background for most currently used methods for potential of mean force calculation is described, including particle insertion, thermodynamic integration, umbrella sampling, metadynamics, adaptive biasing force and milestoning. A brief comparison of strengths and weaknesses of the competing approaches is presented. This is followed by a survey of results obtained by the different methods, with special attention to describing the mechanistic insights generated by modelling and illustrating capabilities of the different techniques. We conclude with a discussion of recent advances and future directions in modelling membrane permeation, including latest methodological enhancements, consideration of multiple slow variables and memory effects. 相似文献
13.
14.
Compared with imidazolium-based ionic liquids (ILs), phosphonium-based ILs have been proven to be more stable in thermodynamics and less expensive to manufacture. In this work, a kind of phosphonium-based IL, [PC6C6C6C14][Tf2N], was studied under several conditions using molecular dynamics simulations based on both the all-atom force field (AAFF) and the united-atom force field. Liquid density was calculated to validate the force field. Compared with experimental data, good agreement was obtained for the simulated density based on the AAFF. Heat capacities at constant pressure were calculated at several temperatures, and good linear relationships were observed. Self-diffusion coefficients, viscosities and conductivities were also calculated to study the dynamics properties of this IL. The viscosity of this IL at 293 K was also compared with experimental data, and the error was in a reasonable range. In order to depict the microstructures of the IL, centre-of-mass and site-to-site radial distribution functions were employed. In addition, spatial distribution functions were investigated to present the more intuitive features. 相似文献
15.
Irene M.C. van AmsterdamMarcellus Ubbink Gerard W. Canters 《Inorganica chimica acta》2002,331(1):296-302
We have constructed a disulfide dimer of S118C azurin, in which two copper centers are coupled through a relatively short covalent pathway, and studied its electron transfer properties. The dimer exhibits intriguing mechanistic properties. Due to the strain in the molecule, caused by the limited accessibility of Cys118, anti-cooperativity occurs in the two step oxidation of the dimer with a difference in redox potential between the two half reactions of 33 mV. Upon oxidation, the dimer favours the semi-reduced over the fully oxidized state, as the Cu(I) site in the semi-reduced dimer is able to stabilize the strained dimer complex. The internal electron transfer is surprisingly slow, which could be partially due to an increase in reorganization energy. 相似文献
16.
黄素氧化还原蛋白（flavodoxin,Fld）是一类通过非共价键与黄素单核苷酸（flavinmononucleotide,FMN）紧密结合的小黄素蛋白,在原核生物及低等真核生物中作为重要的低电势电子传递载体参与了众多的生化反应。在Fld的结构和分类、FMN与脱辅基Fld结合途径以及Fld结构与功能的关系等方面综述了近年来的相关研究进展。 相似文献
17.
Molecular dynamics simulations were carried out to calculate free energy differences between the folded and unfolded states of wild type and mutant collagen model peptides. The calculated stability of the collagen models was compared with the severity of osteogenesis imperfecta. Free energy differences of Gly → Xaa (Xaa: Ser, Cys, Glu, and Asp) mutations between the wild type and the mutants at position 15 of the model peptide were 3.8, 4.2, 5.6, and 8.8 kcal/mol, respectively. The corresponding free energy differences of a second Gly mutation at the same position in different chains were, on average, 1.3, 1.5, 2.9, and 5.4 kcal/mol, respectively. Free energy simulations were also performed to estimate the relative stability between an oxidized form and a reduced form of the mutants containing two Cys residues, which indicated that the mutant of the collagen-like peptide containing an intramolecular disulfide bond was more stable than the mutant containing one Cys residue but less stable than the wild type. The calculated free energy differences between an oxidized and a reduced form of the mutants containing two Cys residues are 0.8 and 2.6 kcal/mol for the disulfide bonds between Chains A and B and between Chains A and C, respectively. 相似文献
18.
《Proteins》2018,86(4):414-422
CaV channels are transmembrane proteins that mediate and regulate ion fluxes across cell membranes, and they are activated in response to action potentials to allow Ca2+ influx. Since ion channels are composed of charge or polar groups, an external alternating electric field may affect the ion‐selective membrane transport and the performance of the channel. In this article, we have investigated the effect of an external GHz electric field on the dynamics of calcium ions in the selectivity filter of the CaVAb channel. Molecular dynamics (MD) simulations and the potential of mean force (PMF) calculations were carried out, via the umbrella sampling method, to determine the free energy profile of Ca2+ ions in the CaVAb channels in presence and absence of an external field. Exposing CaVAb channel to 1, 2, 3, 4, and 5 GHz electric fields increases the depth of the potential energy well and this may result in an increase in the affinity and strength of Ca2+ ions to binding sites in the selectivity filter the channel. This increase of strength of Ca2+ ions binding in the selectivity filter may interrupt the mechanism of Ca2+ ion conduction, and leads to a reduction of Ca2+ ion permeation through the CaVAb channel. 相似文献
19.
Shifts in the absorption bands of bacteriochlorophyll and carotenoids in Chromatium vinosum chromatophores were measured after short actinic flashes, under various conditions. The amplitude of the bacteriochlorophyll band shift correlated well with the amount of cytochrome c-555 that was oxidized by P870+ after a flash. No bacteriochlorophyll band shift appeared to accompany the photooxidation of P870 itself, nor the oxidation of cytochrome c-552 by P870+. The carotenoid band shift also correlated with cytochrome c-555 photooxidation, although a comparatively small carotenoid shift did occur at high redox potentials that permitted only P870 oxidation.
The results explain earlier observations on infrared absorbance changes that had suggested the existence of two different photochemical systems in Chromatium. A single photochemical system accounts for all of the absorbance changes.
Previous work has shown that the photooxidations of P870 and cytochrome c-555 cause similar changes in the electrical charge on the chromatophore membrane. The specific association of the band shifts with cytochrome c-555 photooxidation therefore argues against interpretations of the band shifts based on a light-induced membrane potential. 相似文献
20.
Martin Matas 《Molecular simulation》2017,43(17):1436-1441
The paper deals with the methodology of film growth simulations using classical molecular dynamics and an empirical interaction potential. We focus on the effect of the cut-off distance (rC) of the short-range part of the potential. On the one hand, we find that rC does not affect the qualitative conclusions of the simulations and that its quantitative effect is in the logical direction (better crystallinity at higher rC). On the other hand, we show that the aforementioned quantitative effect is very strong, and clearly underestimated in the literature. The film crystallinity is affected by (non-)neglecting of as seemingly low energies as several meV per bond. The results are important for the design of growth simulations of crystalline films and for the correct interpretation of their results. 相似文献