Cholesterol inhibits oxygen permeation through biological membranes: mechanism against double-bond peroxidation.

The presence of oxygen molecules (O2) in biological membranes promotes lipid peroxidation of phospholipids with unsaturated acyl chains. On the other hand, cholesterol is considered to be an antioxidant molecule as it has a significant barrier effect on the permeation of O2 across membranes. However, a comprehensive explanation of how cholesterol affects the distribution and diffusion of O2 within lipid bilayers is yet to be established. In this study, we investigated the interaction of oxygen molecules with polyunsaturated lipid bilayers using molecular dynamics (MD) simulations. The degree of lipid unsaturation and the concentration of cholesterol were varied to study the permeation of O2. The free energy profile of O2 diffusing from the water phase to the lipid bilayer was calculated using biased umbrella MD simulations. The results show that O2 passively translocates into the membrane without changing the physical properties of the bilayer. Interestingly, in the unsaturated lipid bilayers the presence of cholesterol led to a significantly decreased permeation of O2 and an increase in the lipid chain order. Our results indicate that the hydroxyl groups of cholesterol strongly interact with the O2 molecules effectively inhibiting interactions between the oxygens and the double bonds in unsaturated lipid tails. In addition, a linear relationship between permeation and the ratio of membrane thickness and area per lipid was found. These insights can help our understanding of how the degree of unsaturation in a lipid tail and cholesterol affect lipid peroxidation at the molecular level.

Pore Formation by Amyloid-like Peptides: Effects of the Nonpolar-Polar Sequence Pattern.

One of the mechanisms accounting for the toxicity of amyloid peptides in diseases like Alzheimer's and Parkinson's is the formation of pores on the plasma membrane of neurons. Here, we perform unbiased all-atom simulations of the full membrane damaging pathway, which includes adsorption, aggregation, and perforation of the lipid bilayer accounting for pore-like structures. Simulations are performed using four peptides made with the same amino acids. Differences in the nonpolar-polar sequence pattern of these peptides prompt them to adsorb into the membrane with the extended conformations oriented either parallel [peptide labeled F1, Ac-(FKFE)2-NH2], perpendicular (F4, Ac-FFFFKKEE-NH2), or with an intermediate orientation (F2, Ac-FFKKFFEE-NH2, and F3, Ac-FFFKFEKE-NH2) in regard to the membrane surface. At the water-lipid interface, only F1 fully self-assembles into ß-sheets, and F2 peptides partially fold into an α-helical structure. The ß-sheets of F1 emerge as electrostatic interactions attract neighboring peptides to intermediate distances where nonpolar side chains can interact within the dry core of the bilayer. This complex interplay between electrostatic and nonpolar interactions is not observed for the other peptides. Although ß-sheets of F1 peptides are mostly parallel to the membrane, some of their edges penetrate deep inside the bilayer, dragging water molecules with them. This precedes pore formation, which starts with the flow of two water layers through the membrane that expand into a stable cylindrical pore delimited by polar faces of ß-sheets spanning both leaflets of the bilayer.

Effect of oxidation on POPC lipid bilayers: anionic carboxyl group plays a major role.

Phospholipids with unsaturated acyl chains are major targets of reactive oxygen species leading to formation of oxidized lipids. Oxidized phospholipids have a pronounced role in cell membrane damage. We investigated the effect of oxidation on physiological properties of phospholipid bilayers using atomistic molecular dynamics simulations. We studied phospholipid bilayer systems of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and its two stable oxidized products, 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine (PoxnoPC) and 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC). Structural properties of the POPC lipid bilayer upon the addition of PoxnoPC or PazePC with concentration ranging from 10% to 30% were described. The key finding is that PazePC lipids bend their polar tails toward the bilayer-water interface whereas PoxnoPC lipids orient their tail toward the bilayer interior. The bilayer thickness decreases such that the thickness reduction in bilayers containing PazePC is stronger than in bilayers containing PoxnoPC. The average area per lipid decreases with a stronger effect in bilayers containing PoxnoPC. The addition of PoxnoPC makes both POPC acyl chains slightly more ordered whereas the addition of PazePC reduces the order in the two POPC acyl chains. These structural changes lead to an enhancement in the permeabilities of the bilayers containing these two oxidized products depending on the type, and the amount of oxidation. This enhancement can be achieved with a lower concentration of PazePC (10% or 15%), whereas a higher concentration of PoxnoPC (20%) is required to achieve an apparent enhancement in permeability. While the permeability of bilayers containing PazePC is higher than bilayers containing PoxnoPC in the 10-20% concentration range, by increasing the concentration of the oxidized products to higher than 20%, permeability of the bilayers containing PazePC is reduced such that it is slightly smaller than those containing PoxnoPC.

Biophysical Interpretation of Evolutionary Consequences on the SARS-CoV2 Main Protease through Molecular Dynamics Simulations and Network Topology Analysis.

In this study, we present a combined analysis procedure between atomistic molecular dynamics (MD) simulations and network topology to obtain more understanding on the evolutionary consequences on protein stability and substrate binding of the main protease enzyme of SARS-CoV2. Communicability matrices of the protein residue networks (PRNs) were extracted from MD trajectories of both Mpro enzymes in complex with the nsp8/9 peptide substrate to compare the local communicability within both proteases that would affect the enzyme function, along with biophysical details on global protein conformation, flexibility, and contribution of amino acid side chains to both intramolecular and intermolecular interactions. The analysis displayed the significance of the mutated residue 46 with the highest communicability gain to the binding pocket closure. Interestingly, the mutated residue 134 with the highest communicability loss corresponded to a local structural disruption of the adjacent peptide loop. The enhanced flexibility of the disrupted loop connecting to the catalytic residue Cys145 introduced an extra binding mode that brought the substrate in proximity and could facilitate the reaction. This understanding might provide further help in the drug development strategy against SARS-CoV2 and prove the capability of the combined techniques of MD simulations and network topology analysis as a "reverse" protein engineering tool.

Fullerenes' Interactions with Plasma Membranes: Insight from the MD Simulations.

Understanding the interactions between carbon nanoparticles (CNPs) and biological membranes is critically important for applications of CNPs in biomedicine and toxicology. Due to the complexity and diversity of the systems, most molecular simulation studies have focused on the interactions of CNPs and single component bilayers. In this work, we performed coarse-grained molecular dynamic (CGMD) simulations to investigate the behaviors of fullerenes in the presence of multiple lipid components in the plasma membranes with varying fullerene concentrations. Our results reveal that fullerenes can spontaneously penetrate the plasma membrane. Interestingly, fullerenes prefer to locate themselves in the region of the highly unsaturated lipids that are enriched in the inner leaflet of the plasma membrane. This causes fullerene aggregation even at low concentrations. When increasing fullerene concentrations, the fullerene clusters grow, and budding may emerge at the inner leaflet of the plasma membrane. Our findings suggest by tuning the lipid composition, fullerenes can be loaded deeply inside the plasma membrane, which can be useful for designing drug carrier liposomes. Moreover, the mechanisms of how fullerenes perturb multicomponent cell membranes and how they directly enter the cell are proposed. These insights can help to determine fullerene toxicity in living cells.

Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations.

The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0-32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.

Role of cholesterol flip-flop in oxidized lipid bilayers.

We performed a series of molecular dynamics simulations of cholesterol (Chol) in nonoxidized 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) bilayer and in binary mixtures of PLPC-oxidized-lipid-bilayers with 0-50% Chol concentration and oxidized lipids with hydroperoxide and aldehyde oxidized functional groups. From the 60 unbiased molecular dynamics simulations (total of 161 µs), we found that Chol inhibited pore formation in the aldehyde-containing oxidized lipid bilayers at concentrations greater than 11%. For both pure PLPC bilayer and bilayers with hydroperoxide lipids, no pores were observed at any Chol concentration. Furthermore, increasing cholesterol concentration led to a change of phase state from the liquid-disordered to the liquid-ordered phase. This condensing effect of Chol was observed in all systems. Data analysis shows that the addition of Chol results in an increase in bilayer thickness. Interestingly, we observed Chol flip-flop only in the aldehyde-containing lipid bilayer but neither in the PLPC nor the hydroperoxide bilayers. Umbrella-sampling simulations were performed to calculate the translocation free energies and the Chol flip-flop rates. The results show that Chol's flip-flop rate depends on the lipid bilayer type, and the highest rate are found in aldehyde bilayers. As the main finding, we shown that Chol stabilizes the oxidized lipid bilayer by confining the distribution of the oxidized functional groups.

The Relationship between the Morphology and Elasticity of Natural Rubber Foam Based on the Concentration of the Chemical Blowing Agent.

Concentrated natural latex was used to produce a rubber foam that is porous, elastic and well ventilated. The mechanical properties can be either soft or firm, depending on the formulation of the latex used. Briefly, concentrated natural latex was mixed with chemical agents to make the rubber foam on a laboratory scale using the Dunlop process. In this work, we changed the concentration of the chemical blowing agent in the latex. The morphological properties of the rubber foam were characterised using scanning electron microscopy, and the mechanical properties, or elasticity, were studied using compression experiments and the Mooney-Rivlin calculation. The results show that the concentration of the chemical blowing agent affects the morphological properties of the rubber foam but not the mechanical properties, indicating the heterogeneous structure of the rubber foam. The thermodynamic parameters (∆G and ∆S) and the internal energy force per compression force (Fu/F) of the rubber foam with various amounts of chemical blowing agent were also investigated. This study could be applied in the foam industry, particularly for pillow, mattress and insulation materials, as the present work shows the possible novel control of the morphological structure of the rubber foam without changing its mechanical properties. The difference in cell sizes could affect the airflow in rubber foam.

Current challenges in thermodynamic aspects of rubber foam.

Natural rubber (NR) foam can be prepared by the Dunlop method using concentrated natural latex with chemical agents. Most previous studies have focused on the thermodynamic parameters of solid rubber in extension. The main objective of this study is to investigate the effect of the NR matrix concentration on the static and dynamic properties of NR foams, especially the new approach of considering the thermodynamic aspects of NR foam in compression. We found that the density and compression strength of NR foams increased with increasing NR matrix concentration. The mechanical properties of NR foam were in agreement with computational modelling. Moreover, thermodynamic aspects showed that the ratio of internal energy force to the compression force, Fu/F, and the entropy, S, increased with increasing matrix concentration. The activation enthalpy, ∆Ha, also increased with increasing matrix concentration in the NR foam, indicating the greater relaxation time of the backbone of the rubber molecules. New scientific concepts of thermodynamic parameters of the crosslinked NR foam in compression mode are proposed and discussed. Our results will improve both the knowledge and the development of rubber foams based on the structure-properties relationship, especially the new scientific concept of the thermodynamical parameters under compression.

In silico and in vitro design of cordycepin encapsulation in liposomes for colon cancer treatment.

Cordycepin or 3'-deoxyadenosine is an interesting anti-cancer drug candidate that is found in abundance in the fungus Cordyceps militaris. It inhibits cellular growth of many cancers including lung carcinoma, melanoma, bladder cancer, and colon cancer by inducing apoptosis, anti-proliferation, anti-metastasis and by arresting the cell cycle. Cordycepin has, however, poor stability and low solubility in water, resulting in loss of its bioactivity. Liposomes can be used to overcome these obstacles. Our aim is to improve cordycepin's anti-colon cancer activity by liposome encapsulation. Cordycepin-encapsulated liposomes were designed and fabricated based on a combination of theoretical and experimental studies. Molecular dynamics (MD) simulations and free energy calculations suggest that phosphatidylcholine (PC) lipid environment is favorable for cordycepin adsorption. Cordycepin passively permeates into PC lipid bilayers without membrane damage and strongly binds to the lipids' polar groups by flipping its deoxyribose sugar toward the bilayer center. Our fabricated liposomes containing 10 : 1 molar ratio of egg yolk PC : cholesterol showed encapsulation efficiency (%EE) of 99% using microfluidic hydrodynamic focusing (MHF) methods. In our in vitro study using the HT-29 colon cancer cell line, cordycepin was able to inhibit growth by induction of apoptosis. Cell viability was significantly decreased below 50% at 125 µg mL-1 dosage after 48 h treatment with non-encapsulated and encapsulated cordycepin. Importantly, encapsulation provided (1) a 2-fold improvement in the inhibition of cancer cell growth at 125 µg mL-1 dosage and (2) 4-fold increase in release time. These in silico and in vitro studies indicate that cordycepin-encapsulated liposomes could be a potent drug candidate for colon cancer therapy.

Formation of aggregates, icosahedral structures and percolation clusters of fullerenes in lipids bilayers: The key role of lipid saturation.

Carbon nanoparticles (CNPs) are attractive materials for a great number of applications but there are serious concerns regarding their influence on health and environment. Here, our focus is on the behavior of fullerenes in lipid bilayers with varying lipid saturations, chain lengths and fullerene concentrations using coarse-grained molecular dynamics (CG-MD) simulations. Our findings show that the lipid saturation level is a key factor in determining how fullerenes behave and where the fullerenes are located inside a lipid bilayer. In saturated and monounsaturated bilayers fullerenes aggregated and formed clusters with some of them showing icosahedral structures. In polyunsaturated lipid bilayers, no such structures were observed: In polyunsaturated lipid bilayers at high fullerene concentrations, connected percolation-like networks of fullerenes spanning the whole lateral area emerged at the bilayer center. In other systems only separate isolated aggregates were observed. The effects of fullerenes on lipid bilayers depend strongly on fullerene aggregation. When fullerenes aggregate, their interactions with the lipid tails change.

Alternative metabolic routes in channeling xylose to cordycepin production of Cordyceps militaris identified by comparative transcriptome analysis.

The responsive mechanism of C. militaris TBRC7358 on xylose utilization was investigated by comparative analysis of transcriptomes, growth kinetics and cordycepin productions. The result showed that the culture grown on xylose exhibited high production yield of cordycepin on dry biomass. Comparing xylose to other carbon sources, a set of significantly up-regulated genes in xylose were enriched in pentose and glucuronate interconversion, and cordycepin biosynthesis. After validating up-regulated genes using quantitative real-time PCR, interestingly, putative alternative 3'-AMP-associated metabolic route on cordycepin biosynthesis was identified. Through reporter metabolites analysis of C. militaris, significant metabolites (e.g., AMP, glycine and L-glutamate) were identified guiding involvement of growth and cordycepin production. These findings suggested that there was a cooperative mechanism in transcriptional control of the supplying precursors pool directed towards the cordycepin biosynthesis through main and putative alternative metabolic routes for leverage of cell growth and cordycepin production on xylose of C. militaris strain TBRC7358.

Molecular dynamics study of natural rubber-fullerene composites: connecting microscopic properties to macroscopic behavior.

Macroscopic and microscopic properties of fullerene (C60)-cis-polyisoprene (cis-PI) composites at varying fullerene concentrations were investigated using atomistic molecular dynamics (MD) simulations over microsecond time scales. Results show that the introduction of fullerenes into a polymer matrix increases density, bulk modulus and heat capacity while thermal expansivity decreases. The presence of fullerenes slowed the diffusion of both C60 and cis-PI. Moreover, increasing fullerene concentration results in ordering of the cis-PI chains at the cis-PI-fullerene interfaces and shrinking of bulk PI regions. Free energy calculations of fullerene dimerization suggest that fullerenes disperse at low and aggregate at high fullerene concentrations. Our multi-scaled analysis approach demonstrates the role of 'ordered' regions adjacent to the interface between cis-PI and fullerene in controlling the level of order and mobility of the cis-PI chains. The relationship between the microscopic behavior and the changes in mechanical and thermal properties are discussed. Our study is beneficial for further studies and development of advanced rubber technology for novel, cost-effective, material with very high stiffness and thermal endurance with optimizing conditions of filler contents.

Molecular mechanism of Forkhead box M1 inhibition by thiostrepton in breast cancer cells.

Breast cancer is the most common type of malignancies in women worldwide, and genotoxic chemotherapeutic drugs are effective by causing DNA damage in cancer cells. However, >90% of patients with metastatic cancer are resistant to chemotherapy. The Forkhead box M1 (FOXM1) transcription factor plays a pivotal role in the resistance of breast cancer cells to chemotherapy by promoting DNA damage repair following genotoxic drug treatment. The aim of the present study was to investigate the inhibition of the FOXM1 protein by thiostrepton, a natural antibiotic produced by the Streptomyces species. Experimental studies were designed to examine the effectiveness of thiostrepton in downregulating FOXM1 mRNA expression and activity, leading to senescence and apoptosis of breast cancer cells. The cytotoxicity of thiostrepton in breast cancer was determined using cell viability assay. Additionally, thiostrepton treatment decreased the mRNA expression of cyclin B1 (CCNB1), a downstream target of FOXM1. The present results indicated that thiostrepton inhibited FOXM1 mRNA expression and its effect on CCNB1. Molecular dynamic simulations were performed to study the interactions between FOXM1­DNA and thiostrepton after molecular docking. The results revealed that the possible mechanism underlying the inhibitory effect of thiostrepton on FOXM1 function was by forming a tight complex with the DNA and FOXM1 via its binding domain. Collectively, these results indicated that thiostrepton is a specific and direct inhibitor of the FOXM1 protein in breast cancer. The findings of the present study may lead to the development of novel therapeutic strategies for breast cancer and help overcome resistance to conventional chemotherapeutic drugs.

Dependence of fullerene aggregation on lipid saturation due to a balance between entropy and enthalpy.

It is well-known that fullerenes aggregate inside lipid membranes and that increasing the concentration may lead to (lethal) membrane rupture. It is not known, however, how aggregation and rupture depend on the lipid type, what physical mechanisms control this behavior and what experimental signatures detect such changes in membranes. In this paper, we attempt to answer these questions with molecular simulations, and we show that aggregation and membrane damage depend critically on the degree of saturation of the lipid acyl chains: unsaturated bonds, or "kinks", impose a subtle but crucial compartmentalization of the bilayer into core and surface regions leading to three distinct fullerene density maxima. In contrast, when the membrane has only fully saturated lipids, fullerenes prefer to be located close to the surface under the head groups until the concentration becomes too large and the fullerenes begin clustering. No clustering is observed in membranes with unsaturated lipids. The presence of "kinks" reverses the free energy balance; although the overall free energy profiles are similar, entropy is the dominant component in unsaturated bilayers whereas enthalpy controls the fully saturated ones. Fully saturated systems show two unique signatures: 1) membrane thickness behaves non-monotonously while the area per lipid increases monotonously. We propose this as a potential reason for the observations of low fullerene concentrations being effective against bacteria. 2) The fullerene-fullerene radial distribution function (RDF) shows splitting of the second peak indicating the emergence short-range order and the importance of the second-nearest neighbor interactions. Similar second peak splitting has been reported in metal glasses.

Does α-Tocopherol Flip-Flop Help to Protect Membranes Against Oxidation?

α-Tocopherols (α-toc) are crucial in protecting biological membranes against oxidation by free radicals. We investigate the behavior of α-toc molecules in lipid bilayers containing oxidized lipids by molecular dynamics (MD) simulations. To verify the approach, the location and orientation of α-toc are first shown to be in agreement with previous experimental results. The simulations further show that α-toc molecules stay inside the lipid bilayer with their hydroxyl groups in contact with the bilayer surface. Interestingly, interbilayer α-toc flip-flop was observed in both oxidized and nonoxidized bilayers with significantly higher frequency in aldehyde lipid bilayer. Free-energy calculations were performed, and estimates of the flip-flop rates across the bilayers were determined. As the main finding, our results show that the presence of oxidized lipids leads to a significant decrease of free-energy barriers and that the flip-flop rates depend on the type of oxidized lipid present. Our results suggest that α-toc molecules could potentially act as high-efficacy scavengers of free radicals to protect membranes from oxidative attack and help stabilize them under oxidative stress.

A molecular dynamics study of conformations of beta-cyclodextrin and its eight derivatives in four different solvents.

Understanding the atomic level interactions and the resulting structural characteristics is required for developing beta-cyclodextrin (ßCD) derivatives for pharmaceutical and other applications. The effect of four different solvents on the structures of the native ßCD and its hydrophilic (methylated ßCD; MEßCD and hydroxypropyl ßCD; HPßCD) and hydrophobic derivatives (ethylated ßCD; ETßCD) was explored using molecular dynamics (MD) simulations and solvation free energy calculations. The native ßCD, 2-MEßCD, 6-MEßCD, 2,6-DMßCD, 2,3,6-TMßCD, 6-HPßCD, 2,6-HPßCD and 2,6-ETßCD in non-polar solvents (cyclohexane; CHX and octane; OCT) were stably formed in a symmetric cyclic cavity shape through their intramolecular hydrogen bonds. In contrast, ßCDs in polar solvents (methanol; MeOH and water; WAT) exhibited large structural changes and fluctuations leading to significant deformations of their cavities. Hydrogen bonding with polar solvents was found to be one of the major contributors to this behavior: solvent-ßCD hydrogen bonding strongly competes with intramolecular bonding leading to significant changes in the structural stability of ßCDs. An exception to this is the hydrophobic 2,6-ETßCD which retained its spherical cavity in all solvents. Based on this, it is proposed that the 2,6-ETßCD can act as a sustained release drug carrier.

Alpha-tocopherol inhibits pore formation in oxidized bilayers.

In biological membranes, alpha-tocopherols (α-toc; vitamin E) protect polyunsaturated lipids from free radicals. Although the interactions of α-toc with non-oxidized lipid bilayers have been studied, their effects on oxidized bilayers remain unknown. In this study, atomistic molecular dynamics (MD) simulations of oxidized lipid bilayers were performed with varying concentrations of α-toc. Bilayers with 1-palmitoyl-2-lauroyl-sn-glycero-3-phosphocholine (PLPC) lipids and their aldehyde derivatives at a 1 : 1 ratio were studied. Our simulations show that oxidized lipids self-assemble into aggregates with a water pore rapidly developing across the bilayer. The free energy of transporting an α-toc molecule in a bilayer suggests that α-tocs can passively adsorb into it. When α-toc molecules were present at low concentrations in bilayers containing oxidized lipids, water pore formation was slowed down. At high α-toc concentrations, no pores were observed. Based on the simulations, we propose that the mechanism of how α-toc inhibits pore formation in bilayers with oxidized lipids is the following: α-tocs trap the polar groups of the oxidized lipids at the membrane-water interface resulting in a decreased probability of the oxidized lipids making contact with the two leaflets and initiating pore formation. This demonstrates that α-toc molecules not only protect the bilayer from oxidation but also help to stabilize the bilayer after lipid peroxidation occurs. These results will help in designing more efficient molecules to protect membranes from oxidative stress.

Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study.

Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H(+)-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.

The good, the bad and the user in soft matter simulations.

Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.