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By allowing coal to be converted by microorganisms into products like methane, hydrogen, methanol, ethanol, and other products, current coal deposits can be used effectively, cleanly, and sustainably. The intricacies of in situ microbial coal degradation must be understood in order to develop innovative energy production strategies and economically viable industrial microbial mining. This review covers various forms of conversion (such as the use of MECoM, which converts coal into hydrogen), stresses, and in situ use. There is ongoing discussion regarding the effectiveness of field-scale pilot testing when translated to commercial production. Assessing the applicability and long-term viability of MECoM technology will require addressing these knowledge gaps. Developing suitable nutrition plans and utilizing lab-generated data in the field are examples of this. Also, we recommend directions for future study to maximize methane production from coal. Microbial coal conversion technology needs to be successful in order to be resolved and to be a viable, sustainable energy source. [ABSTRACT FROM AUTHOR]

Wastewater monitoring for SARS-CoV-2 is a valuable tool for surveillance in public health. However, reliable analytical methods and appropriate approaches for the normalization of results are important requirements for implementing state-wide monitoring programs. In times of insufficient case reporting, the evaluation of wastewater data is challenging. Between December 2021 and July 2022, we analyzed 646 samples from 23 WWTPs in Thuringia, Germany. We investigated the performance of a direct capture-based method for RNA extraction (4S-method) and evaluated four normalization methods (NH4-N, COD, Ntot, and PMMoV) in a pooled analysis using different epidemiological metrics. The performance requirements of the 4S method were well met. The method could be successfully applied to implement a state-wide wastewater monitoring program including a large number of medium and small wastewater treatment plants (<100,000 p.e) in high spatial density. Correlations between wastewater data and 7-day incidence or 7-day-hospitalization incidence were strong and independent from the normalization method. For the test positivity rate, PMMoV-normalized data showed a better correlation than data normalized with chemical markers. In times of low testing frequency and insufficient case reporting, 7-day-incidence data might become less reliable. Alternative epidemiological metrics like hospital admissions and test positivity data are increasingly important for evaluating wastewater monitoring data and normalization methods. Furthermore, future studies need to address the variance in biological replicates of wastewater. [ABSTRACT FROM AUTHOR]

This study investigates the degradation characteristics of chlorpyrifos under individual exposure and compound exposure to multiple pesticides in both traditional constructed wetlands and electrochemically constructed wetland coupled systems, while also analyzing the microbial communities within the systems using high-throughput sequencing technology. The results show that the electric field can enhance the degradation performance of the system. The degradation effect of the coupled electrochemically constructed wetland coupled system is better than that of the traditional constructed wetland, while the compound exposure to multiple pesticides inhibits the degradation efficiency. Under the influence of pesticides, the diversity of microbial communities decreases towards the end of the system operation, and the electrochemically constructed wetland coupled system exhibits lower diversity compared to the traditional constructed wetland. Proteobacteria is the dominant phylum under compound exposure to multiple pesticides, while Firmicutes, Fusobacteria, Verrucomicrobia, Aeromonas, and Methylophilus are the dominant electrochemically active phyla and genera in the electrochemically constructed wetland coupled system. The impact of pesticides and the electric field results in a decrease in amino acid metabolism and carbohydrate metabolism functions, while membrane transport functions increase. The compound exposure to multiple pesticides has a more significant impact on the microbial community structure and functionality than the electric field. The results also lay a theoretical foundation for the expansion of pesticide degradation technology and constructed wetland treatment technology to new fields, which is of great significance in realizing the "zero direct discharge" of agricultural production wastewater, solving the problem of agricultural non-point source pollution and ensuring the availability of agricultural production. [ABSTRACT FROM AUTHOR]

The biodegradability of water hyacinth for biogas and biofertilizer production was studied under mesophilic conditions. The effects of water hyacinth pretreatments were also included in this investigation. It was found that water hyacinth has a low biodegradability of 27% when monodigested, while in a 3:1 ratio with cow manure, the biodegradability increases to 46%. At this elevated biodegradability, the water hyacinth biomethane potential was 185 LCH4/kgVS, while that of cow manure was 216 LCH4/kgVS. The Gompertz kinetic model had superior parameters than the logistic model for most of the water hyacinth–cow manure combined substrate digestion. Based on the Gompertz model, the lag phase and daily maximum methane production rate were 5.5 days and 22.9 mL/day, respectively, for the 3:1 codigestion (R2 of 0.99). These values were 6.7 days and 15.2 mL/day, respectively, in the case of water hyacinth monodigestion (R2 = 0.996). The dominant microbial species detected in the digestates were Bacteroidetes and Proteobacteria. A few microbial species were indigenous to water hyacinth, but more diverse consortia, which are key to efficient substrate biodegradation, came from cow manure. The digestate contained ammonium nitrogen at 68 mg/kg with phosphorous and potassium at 73 and 424 mg/kg, respectively. Nitrogen was lower but phosphorous and potassium were comparable to previously studied digestates of other substrates. Only water hyacinth pretreated by aerobic composting was proven to unlock a higher methane yield that matched the 3:1 codigestion with cow manure. Other pretreatments induced better biodegradation performance than that observed in untreated water hyacinth but these improvements were not as good as that of the 3:1 codigestion scheme. It was concluded that water hyacinth sourced from the Hartbeespoort Dam could be treated by anaerobic digestion to recover biogas and biofertilizer. However, more experiments are required to fully understand and harness the optimisation opportunities available in applying this technology to manage water hyacinths. [ABSTRACT FROM AUTHOR]

Wastewater surveillance has been widely used to track the prevalence of SARS-CoV-2 in communities. Although some studies have investigated the decay of SARS-CoV-2 RNA in wastewater, understanding about its fate during wastewater transport in real sewers is still limited. This study aims to assess the impact of sewer biofilms on the dynamics of SARS-CoV-2 RNA concentration in naturally contaminated real wastewater (raw influent wastewater without extra SARS-CoV-2 virus/gene seeding) using a simulated laboratory-scale sewer system. The results indicated that, with the sewer biofilms, a 90% concentration reduction of the SARS-CoV-2 RNA was observed within 2 h both in wastewater of gravity (GS, gravity-driven sewers) and rising main (RM, pressurized sewers) sewer reactors. In contrast, the 90% reduction time was 8–26 h in control reactors without biofilms. The concentration reduction of SARS-CoV-2 RNA in wastewater was significantly more in the presence of sewer biofilms. In addition, an accumulation of c.a. 260 and 110 genome copies/cm2 of the SARS-CoV-2 E gene was observed in the sewer biofilm samples from RM and GS reactors within 12 h, respectively. These results confirmed that the in-sewer concentration reduction of SARS-CoV-2 RNA in wastewater was likely caused by the partition to sewer biofilms. The need to investigate the in-sewer dynamic of SARS-CoV-2 RNA, such as the variation of RNA concentration in influent wastewater caused by biofilm attachment and detachment, was highlighted by the significantly enhanced reduction rate of SARS-CoV-2 RNA in wastewater of sewer biofilm reactors and the accumulation of SARS-CoV-2 RNA in sewer biofilms. Further research should be conducted to investigate the in-sewer transportation of SARS-CoV-2 and their RNA and evaluate the role of sewer biofilms in leading to underestimates of COVID-19 prevalence in communities. [ABSTRACT FROM AUTHOR]

Anaerobic digestion is considered a beneficial treatment for biogas production (BP). To improve the performance of this bioprocess, the addition of well-selected inocula could be an interesting approach that affects the overall efficiency of the BP. In this study, the reactor performance and energy analysis of liquid-state anaerobic digestion of cattle manure (CM) at high solids concentration (TS%) (94.87%) with six different inocula—two cellulosic (C.I1, C.I2), one lipidic (Li.I), two lactic (La.I1, La.I2), and one saccharidic (Sacc.I)—were investigated. The results showed that inocula improved the biogas production and yield during anaerobic digestion of CM by 109%, 86%, and 52.4%, respectively, when the cellulosic (C.I1), lipidic (Li.I), and lactic (La.I1) inocula were added, compared with the substrate production alone at a substrate/inoculum (S/I) ratio of 5:3 (v/v). The addition of inocula in an appropriate range is useful for the performance of the anaerobic digestion process. In our study, the 16S rRNA sequencing approach was followed to investigate microbial community structure and diversity in the substrate CM and the three inocula that showed a significant improvement in biogas production (C.I1, Li.I, and La.I). The most abundant bacterial populations were found to be Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, with different abundance percentages. Interestingly, C.I1, which resulted in the highest biogas production, showed the dominance of Cyanobacteria (53.44%) belonging mainly to the class Nostocophycidae. This study highlighted the role of inocula in improving biogas production from cattle manure (CM) thanks to their microbial diversity. [ABSTRACT FROM AUTHOR]

Increasing worldwide milk manufacturing and dairy processing resulted in producing more effluents, and thus effective management of wastewater is now the most important issue. This study used a new design of a pilot plant-scale hybrid anaerobic labyrinth-flow bioreactor (AL-FB) to increase the efficiency of anaerobic biodegradation and biogas productivity and improve anaerobic microflora performance. In addition, effluent recirculation was used to boost the treatment of dairy wastewater. Metagenomic analyses of the anaerobic microbial community were performed. It was found that an organic loading rate (OLR) of 4.0–8.0 g COD/L·d contributed to the highest CH4 yield of 0.18 ± 0.01–0.23 ± 0.02 L CH4/g COD removed, which corresponded to a high COD removal of 87.5 ± 2.8–94.1 ± 1.3%. The evenest distribution of the microorganisms' phyla determined the highest biogas production. In all tested samples, Bacteroidetes and Firmicutes abundance was the highest, and Archaea accounted for about 4%. Metagenomic studies showed that methane was mainly produced in acetoclastic methanogenesis; however, higher OLRs were more favorable for enhanced hydrogenotrophic methanogenesis. Effluent recirculation enhanced the overall treatment. Thus, at OLR of 10.0 g COD/L·d, the highest COD removal was 89.2 ± 0.4%, and methane production yield achieved 0.20 ± 0.01 L CH4/g COD removed, which was higher by 25% compared to the achievements without recirculation. [ABSTRACT FROM AUTHOR]

Conformational changes in polyampholyte polypeptides adsorbed on the surface of an oblate metal nanospheroid with a periodic change in time of its polarity along the axis of rotation have been studied using the molecular dynamics method. The radial distributions of polypeptide atoms, as well as the distributions of the linear density of polypeptide atoms along the nanospheroid rotation axis, are constructed. The obtained conformational structures of polyampholytes were compared in the presence and in the absence of sodium and chlorine ions in water. At low temperatures, the formation of a narrow macromolecular ring around the nanospheroid near the equator was observed; the ring swelled with an increase in the amplitude of an external alternating electric field; and polyampholyte desorption occurred with a further increase in the amplitude. At high temperatures, periodic changes in the conformational structure of adsorbed polyampholytic polypeptides were observed on the surface of the oblate metal nanospheroid with the frequency of an external polarizing alternating field. [ABSTRACT FROM AUTHOR]

The agricultural spreading of treated sewage sludge is a valid strategy in terms of circular economy for the management of this nutrient-rich waste. Anaerobic digestion (AD) can be applied to stabilize and hygienize sewage sludge, making it suitable for agricultural reuse, while producing biogas to be utilized as an energy vector. However, the presence of contaminants, including petroleum hydrocarbons, could limit the widespread agricultural utilization of sewage sludge. In this context, the impact of dewatering agents, such as cationic polyelectrolytes, on AD efficiency and hydrocarbon biodegradation has been poorly investigated, although it represents a noteworthy aspect when conditioned sludge is digested for agricultural use in centralized biogas plants. This work aims to elucidate the effect of cationic polyelectrolyte addition on biomethanation as well as the degradation and extractability of C10-C40 hydrocarbons during mesophilic AD of sewage sludge. The addition of 26.7 g/kgTS of cationic polyelectrolyte was observed to extend the AD lag phase, although similar methane yields (573–607 mLCH4 per g of degraded volatile solids) were observed for both conditioned and raw sludge. Furthermore, a significant impact on hydrocarbon degradation was observed due to chemical conditioning. Indeed, this work reveals that cationic polyelectrolytes can affect hydrocarbon extractability and suggests moreover that the presence of natural interferents (e.g., biogenic waxes) in sewage sludge may lead to an overestimation of potentially toxic C10-C40 hydrocarbon concentrations, potentially limiting the application of sludge-derived digestates in agriculture. [ABSTRACT FROM AUTHOR]

Anaerobic digestion is a common procedure of treating sewage sludge at wastewater treatment plants. However, plants differ in terms of the number of reactors and, in case of several reactors, their operation mode. To confirm the flexibility of well adapted, full-scale anaerobic digestion plants, we monitored the physicochemical process conditions of two continuously stirred tank reactors over one hydraulic retention time before and after the operation mode was switched from parallel to serial operation. To investigate changes in the involved microbiota, we applied Illumina amplicon sequencing. The rapid change between operation modes did not affect the process performance. In both parallel and serial operation mode, we detected a highly diverse microbial community, in which Bacteroidetes, Firmicutes, Proteobacteria and Claocimonetes were high in relative abundance. While a prominent core microbiome was maintained in both configurations, changes in the involved microbiota were evident at a lower taxonomical level comparing both reactors and operation modes. The most prominent methanogenic Euryarchaeota detected were Methanosaeta and cand. Methanofastidiosum. Volatile fatty acids were degraded immediately in both reactors, suggesting that the second reactor could be used to produce methane on demand, by inserting easily degradable substrates. [ABSTRACT FROM AUTHOR]

A problem has been considered concerning the study of the formation of a macromolecular fringe layer of a polyampholyte chain adsorbed on the surface of a metal flattened nanospheroid, which either carries an excess electrical charge or is polarized by an external uniform field. For this system, a mathematical model has been proposed, which takes into account the entropy-related effect of the formation of different conformations of a Gaussian chain on the curved surface and the interaction of dipoles of chain segments with the field of the charged or polarized conducting nanospheroid. Molecular dynamics has been employed to study electrically induced conformational changes in polyampholytic polypeptides having different distances between oppositely charged units in a macrochain adsorbed on the surface of a flattened gold nanospheroid, which is either charged or polarized along its rotation axis. The distributions of the average linear density along the rotation axis and the radial distributions of the average density in the equatorial region of the nanospheroid have been calculated. On the surface of the charged flattened metal nanospheroid, macrochain loops are predominantly oriented in the direction of the nanospheroid rotation axis, as the distance between charged units in a macrochain increases. On the surface of a flattened nanospheroid polarized along the rotation axis in an external electric field, the macromolecular fringe swells in both the polar regions and the equatorial region of the nanospheroid, with the swelling being caused by the formation of macromolecular loops of two types. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation has been employed to study rearrangements in the conformational structure of polyelectrolytic polypeptides adsorbed on the surface of a charged prolate spheroidal gold nanoparticle, as well as such nanoparticle polarized along its major axis. An analytical model has been proposed for the structure of a Gaussian macrochain adsorbed on the spheroidal nanoparticle. The model reflects the features of the structure formation of the adsorbed macrochain in relation to the geometry of the uncharged and unpolarized prolate spheroidal nanoparticle. When necessary, it takes into account the surface charge or polarization of the particle by means of introducing the Boltzmann factor for equilibrium configurations of the macrochain in a potential field. Polyampholitic polypeptides adsorbed on the surface of the polarized prolate metal nanospheroid are swollen in the polar regions, while the units of uniformly charged polypeptides are shifted to the polar regions charged oppositely to the charge of the units. Being adsorbed on the surface of a charged prolate spheroidal gold nanoparticle, a polyelectrolyte macromolecule envelopes the entire nanoparticle and swells with an increase in the total charge of the nanospheroid. [ABSTRACT FROM AUTHOR]

Molecular dynamics has been employed to study conformational rearrangements of polyampholytic and uniformly charged polypeptides adsorbed on the surface of a transversely polarized nanowire, in particular, upon rotation of the polarizing electric field vector. On the surface of the transversely polarized nanowire, a fringe consisting of polyampholitic polypeptide macromolecules is protruded in the direction of polarization, while uniformly charged polypeptide is shifted to the polarized regions of the cross section that are charged oppositely to the charge of macrochain units. The larger the distance between oppositely charged units in the polyampholytic polypeptide, the higher the ratio between the fringe thicknesses in the direction of polarization and in the orthogonal direction in the cross section plane. In an electric field rotating around the axis of the metal nanowire, uniformly charged polypeptides adsorbed on its surface rotate around the wire in the same direction. The same phenomenon has been observed for polyampholytic polypeptides, in which the distances between negatively and positively charged units in macrochains are longer than the half-circumference of the nanowire. [ABSTRACT FROM AUTHOR]

Molecular dynamics has been employed to study conformational rearrangements of polyampholytic polypeptides adsorbed on the surface of a metal nanoparticle, with the rearrangements being caused by changes in the direction of particle polarization at a frequency corresponding to microwave electric field. The time dependences of the dipole moments, as well the radial and angular density distributions of adsorbed polypeptide atoms upon the prepolarization of the nanoparticle, have been calculated. The rearrangements occurring in the conformational structure of a polyampholytic polypeptide adsorbed on the nanoparticle upon periodic changes in the particle polarization direction are accompanied by two effects: fluctuations in the conformational structure of the polypeptide and the formation of a ring of macromolecules in the equatorial region of the nanoparticle. [ABSTRACT FROM AUTHOR]

Molecular dynamics has been employed to study rearrangements in the conformational structure of polyampholytic macrochains with different distributions of charged units in the electric field of a polarized metal nanoparticle. The angular and radial distributions have been calculated for the average densities of polypeptide atoms. The radial distributions of the average density of polypeptide atoms have been obtained in the vicinities of the positively and negatively charged poles of the nanoparticle, as well as in its equatorial region. An analytical model has been proposed for conformational rearrangements of an adsorbed macrochain in the field of the polarized nanoparticle. The formation a nonuniform distribution of the density of polypeptide atoms has been analyzed as depending on the angle between the directions of the dipole moment vector and the vector of the normal to the nanoparticle surface. Swelling of the macromolecular "fringe" has been observed with the predominant protrusion of loops in the direction of the polarization axis. [ABSTRACT FROM AUTHOR]

The application of anaerobic digestors to decentralized wastewater treatment systems (DWTS) has gained momentum worldwide due to their ease of operation, high efficiency, and ability to recycle wastewater. However, the microbial mechanisms responsible for the high efficiency and ability of DWTS to recycle wastewater are still unclear. In this study, the microbial community structure and function of two different anaerobic bioreactors (a primary sludge digestor, PSD, and anaerobic membrane bioreactor, AnMBR) of a DWTS located in Germany was investigated using 16S rRNA gene amplicon and metagenomic sequencing, respectively. The results showed that the microbial community structure was remarkably different in PSD and AnMBR. Methanobacteriaceae and Syntrophaceae were identified as the families that significantly differed in abundance between these two bioreactors. We also used genome-centered metagenomics to predict the microbial interactions and methane-generating pathway, which yielded 21 near-complete assembled genomes (MAGs) (average completeness of 93.0% and contamination of 2.9%). These MAGs together represented the majority of the microbial community. MAGs affiliated with methanogenic archaea, including Methanobacterium sp., Methanomicrobiales archaea, Methanomassiliicoccales archaea, and Methanosaeta concilii, were recruited, along with other syntrophic bacterial MAGs associated with anaerobic digestion. Key genes encoding enzymes involved in specific carbohydrate-active and methanogenic pathways in MAGs were identified to illustrate the microbial functions and interactions that occur during anaerobic digestion in the wastewater treatment. From the MAG information, it was predicted that bacteria affiliated with Bacteroidetes, Prolixibacteraceae, and Synergistaceae were the key bacteria involved in anaerobic digestion. In the methane production step, Methanobacterium sp. performed hydrogenotrophic methanogenesis, which reduced carbon dioxide to methane with hydrogen as the primary electron donor. Taken together, our findings provide a clear understanding of the methane-generating pathways and highlight the syntrophic interactions that occur during anaerobic digestion in DWTS. [ABSTRACT FROM AUTHOR]

Molecular dynamics has been employed to study conformational changes of polyampholytic polypeptides on the surface of a spherical gold nanoparticle at different surface charge densities, including the case of the presence of eosin Y anions adsorbed on polypeptide macrochains. Equilibrium conformations have been determined for polyampholytic polypeptides adsorbed of a spherical gold nanoparticle. Radial distributions of the concentration of atoms of polyampholytic polypeptides on the gold nanoparticle have been plotted with differentiation over the types of units at different surface charge densities. Corresponding distributions have also been obtained for dye anions adsorbed on polypeptide macrochains. The results obtained may be used for the development and modification of sensors with tunable conformational structures of macrochains, such as luminescent optical testers for the concentration of molecular oxygen (including singlet oxygen) and chemical sensors based on the effects of surface plasmon resonance and surface-enhanced Raman scattering. [ABSTRACT FROM AUTHOR]

Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role. [ABSTRACT FROM AUTHOR]

Aims: To elucidate how granular sludge inoculum and particle-rich organic loading affect the structure of the microbial communities and process performance in upflow anaerobic sludge bed (UASB) reactors. Methods and Results: We investigated four reactors run on dairy manure filtrate and four on pig manure supernatant for three months achieving similar methane yields. The reactors fed with less particle rich pig manure stabilized faster and had highest capacity. Microbial community dynamics analysed by a PCR/denaturing gradient gel electrophoresis approach showed that influent was a major determinant for the composition of the reactor communities. Comparisons of pre- and non-adapted inoculum in the reactors run on pig manure supernatant showed that the community structure of the nonadapted inoculum adapted in approximately two months. Microbiota variance partitioning analysis revealed that running time, organic loading rate and inoculum together explained 26 and 31% of the variance in bacterial and archaeal communities respectively. Conclusions: The microbial communities of UASBs adapted to the reactor conditions in treatment of particle rich manure fractions, obtaining high capacity, especially on pig manure supernatant. Significance and Impact of the Study: These findings provide relevant insight into the microbial community dynamics in startup and operation of sludge bed reactors for methane production from slurry fractions, a major potential source of biogas. [ABSTRACT FROM AUTHOR]

The present work employed a molecular dynamics method to investigate the effect of NaCl concentration on the deformation, breakup, and evaporation characteristics of bio-nanodroplets under a strong electric field. It aims to reveal the size control mechanism for a nanoparticle produced by electrospray deposition. The results show that when the droplet dissolves NaCl, it is elongated to be a longer “spindle” by the electric field force, compared to the droplet without NaCl, and several small clusters are ejected from two tips of the spindle due to the hydration effect of Na+and Cl−. In addition, the formation of ion pairs is observed when the droplet dissolves NaCl. The NaCl concentration affects the hydration degree and the formation of ion pairs significantly, which leads to different spindle lengths and number of clusters. The longer spindle and the larger cluster number could enlarge the free surface area and remarkably accelerate evaporation. Fabrication of smaller bio-nanoparticle requires both a faster evaporation rate and larger cluster number, which can be achieved by selecting an appropriate NaCl concentration. [ABSTRACT FROM AUTHOR]

Biological functions are intimately rooted in biopolymer dynamics. It is commonly accepted that proteins can be considered as complex systems, but the origin of such complexity is still not fully understood. Moreover, it is still not really clear if proteins are true complex systems or complicated ones. Here, molecular dynamics simulations on a two helix bundle protein have been performed, and protein trajectories have been analyzed by using correlation functions in the frequency domain. We show that even a simple protein exhibits the hallmarks of complex systems. Moreover, the molecular bases of this complex behavior are possessed completely by the protein itself, because such complexity emerges without considering the solvent explicitly. © 2012 Wiley Periodicals, Inc. Complexity, 2012 [ABSTRACT FROM AUTHOR]

Lignocellulosic biomass provides a sustainable source of sugars for biofuel and biomaterial production. However, biomass resistance to degradation imposes difficulties for economical conversion of plant carbohydrates to fermentable sugars. One of the key contributors to recalcitrance is lignin. Understanding the properties of lignin macromolecules in the cell wall matrix is useful for manipulating biomass structure to generate more easily degradable biomass. Along with experimental techniques such as 2D-NMR and mass spectrometry, computational techniques can be useful for characterizing the structural and energetic properties of the biomass assembly and its individual constituents. Here, we provide a brief introduction to lignin, review some of the recent, relevant scientific literature, and give our perspectives on the role of molecular simulation in understanding lignin structure. © 2011 American Institute of Chemical Engineers Environ Prog, 2012 [ABSTRACT FROM AUTHOR]

The objective of this study was to prepare and characterize geniposide submicron emulsion (GP-SME) loaded the geniposide phytosomes (GP-PS) geniposide and optimize the process variables. The physicochemical properties of GP-PS obtained were investigated by means of differential scanning calorimetry. A screening experiment with Plackett-Burman design and response surface methodology with Box-Behnken design was used to optimize the process parameters of GP-SME. The optimum process conditions were finally obtained by using a desirability function. The differential scanning calorimetry studies of GP-PS demonstrated that GP and phospholipids in the GP-PS were combined by noncovalent bond, not forming a new compound. A Plackett-Burman design was initially employed and it was found that stirring velocity, homogenization pressure and homogenization cycles were the most important variables that affected the particles size, polydispersity index, and entrapment efficiency of GP-SME. Results showed that the optimum stirring velocity, homogenization pressure, and cycles were 16000 rpm, 50 Mpa, and 10 cycles, respectively. The mean diameter, polydispersity index, and entrapment efficiency of GP-SME were 258.2 nm, 0.243, 72.56%, respectively. [ABSTRACT FROM PUBLISHER]

Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking. [ABSTRACT FROM AUTHOR]

There are several software packages for simulating the main types of biopolymers with molecular dynamics methods. However, work with these packages is rather complicated, especially for experimenters, who are nonexperts in computational structural biology. We have developed GUI-BioPASED, a web-based GUI for the molecular dynamics software BioPASED. This version provides for formulating the task as a single executable file, exporting this file to user’s PC, ensuring its execution, and, thereby, partially automating the task part responsible for the majority of errors. A user-friendly cross-platform interface is created, which performs data check, reports errors, and hints at possible ways to correct them. BioPASED, a general purpose molecular dynamics program, and GUI-BioPASED are described along with a typical example of their usage. [ABSTRACT FROM AUTHOR]

The proton pumping cycle of bacteriorhodopsin consists of five consecutive proton transfer steps, in all of which water molecules are likely to play critical roles. Here we review the role of water molecules in bacteriorhodopsin function, with emphasis on computations of the retinal Schiff base deprotonation reaction and the open questions regarding the participation of water molecules in the longer-distance proton transfer reactions. [ABSTRACT FROM AUTHOR]

Ion channels are part of nature’s solution for regulating biological environments. Every ion channel consists of a chain of amino acids carrying a strong and sharply varying permanent charge, folded in such a way that it creates a nanoscopic aqueous pore spanning the otherwise mostly impermeable membranes of biological cells. These naturally occurring proteins are particularly interesting to device engineers seeking to understand how such nanoscale systems realize device-like functions. Availability of high-resolution structural information from X-ray crystallography, as well as large-scale computational resources, makes it possible to conduct realistic ion channel simulations. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator, offers a powerful and general approach to study ion channel permeation. BioMOCA is based on the Boltzmann Transport Monte Carlo (BTMC) and Particle-Particle-Particle-Mesh (P3M) methodologies developed at the University of Illinois at Urbana-Champaign. In this paper we briefly discuss the various approaches to simulating ion flow in channel systems that are currently being pursued by the biophysics and engineering communities, and present the effect of having anisotropic dielectric constants on ion flow through a number of nanopores with different effective diameters. [ABSTRACT FROM AUTHOR]

High level ab initio studies demonstrate substantial conformational flexibility of amino groups of nucleic acid bases. This flexibility is important for biological functions of DNA. Existing force field models of molecular mechanics do not describe this phenomenon due to a lack of quantitative experimental data necessary for an adjustment of empirical parameters. We have performed extensive calculations of nucleic acid bases at the MP2/6-31G(d,p) level of ab initio theory for broad set of amino group configurations. Two-dimensional maps of energy and geometrical characteristics as functions of two amino hydrogen torsions have been constructed. We approximate the maps by polynomial expressions, which can be used in molecular mechanics calculations. Detailed considerations of these maps enable us to propose a method for determination of numerical coefficients in the developed formulae using restricted sets of points obtained via higher-level calculations. [ABSTRACT FROM AUTHOR]

Proteins in biological nanocomposites play an important role in their mechanical response. Proteins in nacre, the inner layer of seashells, have been shown to have exceptional mechanical properties. One of the important nacre proteins, Lustrin-A, has abundance of polypeptides in zig-zag conformation called β-sheets. β-sheets of protein when present close to each other in multiple numbers could take the shape of a planar β-sheath like structure or a β-barrel to form a domain. In natural proteins both these types of structures are commonly found. However, the conformation of β-sheets in Lustrin-A is not known at this time. Effort has been made through this work to study the mechanical response of these β-planar sheath and β-barrel structures when subjected to external loads. Comparative study of the stress-deformation characteristics of these two types of structures has been made. Both these structures with almost similar number of amino acids have been extracted from one single spinach protein: Ferredoxin Reductase (1FNR). Steered molecular dynamics has been used to conduct these studies. The article deals with the separation of the two domains from the main protein, simulation details, and results comparing the responses. [ABSTRACT FROM AUTHOR]

Pressure is mounting on the pharmaceutical industry to reduce both the cost of drugs and the time to market. The large number of targets made available in the last decade has created a new area for technologies that can rapidly identify quality lead candidates. Virtual screening is one such technology that is gaining increasing importance in the drug discovery process. Virtual screening is a reliable and inexpensive method currently being employed as a complementary approach to high-throughput screening. Virtual screening can be adopted irrespective of the structural information of the target receptor. In the absence of structural data, virtual screening using pharmacophore-based search is a major in silico tool. However, when the structure of the receptor is available, virtual screening using both pharmacophore-based and docking techniques can be employed. Both of these methods can be synergistically integrated to improve the drug design and development process. In this article, we provide an overview of methods for virtual screening--in particular, docking and pharmacophore-based--along with commercial algorithms implementing these methods, and a successful example in this arena. Further, we enumerate the potential for patenting such kind of studies. [ABSTRACT FROM AUTHOR]

The molecular structure of $$\upalpha$$ - l-Rha p-(1→ 2)- $$\upalpha$$ - l-Rha p-OMe has been investigated using conformation sensitive NMR parameters: cross-relaxation rates, scalar 3 J CH couplings and residual dipolar couplings obtained in a dilute liquid crystalline phase. The order matrices of the two sugar residues are different, which indicates that the molecule cannot exist in a single conformation. The conformational distribution function, $$P(\upphi,\uppsi)$$ , related to the two glycosidic linkage torsion angles $$\upphi$$ and $$\uppsi$$ was constructed using the APME method, valid in the low orientational order limit. The APME approach is based on the additive potential (AP) and maximum entropy (ME) models. The analyses of the trajectories generated in molecular dynamics and Langevin dynamics (LD) computer simulations gave support to the distribution functions constructed from the experimental NMR parameters. It is shown that at least two conformational regions are populated on the Ramachandran map and that these regions exhibit very different molecular order. [ABSTRACT FROM AUTHOR]

The parsnip webworm, Depressaria pastinacella, a specialist on two genera in Apiaceae, feeds exclusively on the furanocoumarin-containing reproductive structures of its host plants. This caterpillar relies principally on cytochrome P450-mediated detoxification for coping with the high concentrations of furanocoumarins in its diet. A cDNA encoding the furanocoumarin-inducible P450 CYP6AB3 from this species was coexpressed with house-fly NADPH P450 reductase in baculovirus-infected Sf9 cells and tested for binding and metabolism of the six furanocoumarins typically encountered in host plant tissues. Only imperatorin and bergapten bind in close proximity to the catalytic haem and only imperatorin is metabolized (Vmax and Km of 2.412 pmol/min per pmol P450 and 94.28 µm, respectively). Purification of the imperatorin metabolite by normal phase HPLC and characterization of its structure by MS–MS analysis indicate that CYP6AB3 initially epoxidizes the carbon–carbon pi-bond on the isoprenyl side chain on imperatorin. An improved molecular model for the CYP6AB3 protein based on this biochemical characterization and the recently defined mammalian CYP3A4 crystal structure provides insight into the remarkable substrate specificity of this protein. [ABSTRACT FROM AUTHOR]

Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined. [ABSTRACT FROM AUTHOR]

Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/π interactions. Ab initio interaction energies for 20 carbohydrate–aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from −2.8 to −12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/π interactions and classical H-bonds. The failure of Hartree–Fock method (interaction energies from +1.0 to −6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology. [ABSTRACT FROM AUTHOR]

Cellulose has been used to separate the enantiomers of a range of dimetallo coordination compounds with different surface topologies. The compounds are all approximately cylindrical in shape, but are based on octahedral coordination at the metals and are also helical. When separation has been achieved, the first eluted enantiomer has always been proven to have a negative circular dichroism (CD) signal for its longest wavelength metal to ligand charge transfer band. In order to understand the underlying basis for the elution order, gas phase molecular dynamics and snap‐shot minimisations of each enantiomer with the repeat unit of cellulose, glucose, have been undertaken. For new dimetallo helicates, it is important to have a quick assessment of the enantiomeric identity of the first eluted compound. To this end, the coupled‐oscillator model of CD has been applied to relate the signs of the CD signals to the identity of the enantiomers. This correlation is consistent with crystallographic data for the first eluted enantiomer of the parent compound. [ABSTRACT FROM AUTHOR]

We developed new parameters for molecular dynamics (MD) simulations, namely partial atomic charges, equilibrium bond-lengths, angles, dihedrals, atom types, and force constants of chlorophyll a (Chl) and plastoquinone (PQ), and both reduced and neutral form of primary acceptor (PHO) molecule. These parameters are essential for MD simulations that can interpret various structure functional relationships during primary processes of charge separation and stabilization in photosystem 2 reaction centres. [ABSTRACT FROM AUTHOR]

We have carried out up to 8.0 ns molecular dynamics simulation on the ATP-bound complexes of EGFR and HER-2 (homology model) receptor kinase domains to explore the possible consequences of amino acid residue changes in or close to the ATP site that might provide insights for selectivity of these kinases towards ATP site inhibitors. The simulation results show the formation of a channel under Thr766 following the movement of the side chain of Gln767 away from the hinge in EGFR. In HER-2, a similar movement of Gln799 occurs, but a simultaneous movement of Arg784 towards the hinge region occurs that tends to close the channel. The movement of Arg784 in HER-2 appears to result from the absence of an anchoring residue like Asp746 in EGFR, which has been changed to Gly778 in HER-2. In EGFR, this Arg784 is held away from the hinge region by interaction with Asp746, thereby leaving the channel open. This might be an important contributory factor to differences in selectivity of the ligands between the two kinases, probably more so than the conservative change of Cys751 of EGFR to serine in HER-2 at the ATP site. [ABSTRACT FROM AUTHOR]

We report structural models of the full-length integrase enzyme (IN) of the human immunodeficiency virus type 1 (HIV-1) and its complex with viral and human DNA. These were developed by means of molecular modeling techniques using all available experimental evidence, including X-ray crystallographic and NMR structures of portions of the full-length protein. Special emphasis was placed on obtaining a model of the enzyme’s active site with the viral DNA apposed to it, based on the hypothesis that such a model would allow structure-based design of inhibitors that retain activity in vivo. This was because bound DNA might be present in vivo after 3’-processing but before strand transfer. These structural models were used to study the potential binding modes of various diketo-acid HIV-1 IN inhibitors (many of them preferentially inhibiting strand transfer) for which no experimentally derived complexed structures are available. The results indicate that the diketo-acid IN inhibitors probably chelate the metal ion in the catalytic site and also prevent the exposure of the 3’-processed end of the viral DNA to human DNA. [ABSTRACT FROM AUTHOR]

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method. Last, it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features. [ABSTRACT FROM AUTHOR]

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced. [ABSTRACT FROM AUTHOR]

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson–Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, ΔGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC50 without reparametrization. [ABSTRACT FROM AUTHOR]

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5′-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects. This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing. The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets. [ABSTRACT FROM AUTHOR]

Some key concerns raised by molecular modeling and computational simulation of functional mechanisms for membrane proteins are discussed and illustrated for members of the family of G protein coupled receptors (GPCRs). Of particular importance are issues related to the modeling and computational treatment of loop regions. These are demonstrated here with results from different levels of computational simulations applied to the structures of rhodopsin and a model of the 5-HT2A serotonin receptor, 5-HT2AR. First, comparative Molecular Dynamics (MD) simulations are reported for rhodopsin in vacuum and embedded in an explicit representation of the membrane and water environment. It is shown that in spite of a partial accounting of solvent screening effects by neutralization of charged side chains, vacuum MD simulations can lead to severe distortions of the loop structures. The primary source of the distortion appears to be formation of artifactual H-bonds, as has been repeatedly observed in vacuum simulations. To address such shortcomings, a recently proposed approach that has been developed for calculating the structure of segments that connect elements of secondary structure with known coordinates, is applied to 5-HT2AR to obtain an initial representation of the loops connecting the transmembrane (TM) helices. The approach consists of a simulated annealing combined with biased scaled collective variables Monte Carlo technique, and is applied to loops connecting the TM segments on both the extra-cellular and the cytoplasmic sides of the receptor. Although this initial calculation treats the loops as independent structural entities, the final structure exhibits a number of interloop interactions that may have functional significance. Finally, it is shown here that in the case where a given loop from two different GPCRs (here rhodopsin and 5-HT2AR) has approximately the same length and some degree of sequence identity, the fold adopted by the loops can be similar. Thus, in such special cases homology modeling might be used to obtain initial structures of these loops. Notably, however, all other loops in these two receptors appear to be very different in sequence and structure, so that their conformations can be found reliably only by ab initio, energy based methods and not by homology modeling. [ABSTRACT FROM AUTHOR]

The recent availability of residual dipolar coupling measurements in a variety of different alignment media raises the question to what extent biomolecular structure and dynamics are differentially affected by their presence. A computational method is presented that allows the sensitive assessment of such changes using dipolar couplings measured in six or more alignment media. The method is based on a principal component analysis of the covariance matrix of the dipolar couplings. It does not require a priori structural or dynamic information nor knowledge of the alignment tensors and their orientations. In the absence of experimental errors, the covariance matrix has at most five nonzero eigenvalues if the structure and dynamics of the biomolecule is the same in all media. In contrast, differential structural and dynamic changes lead to additional nonzero eigenvalues. Characteristic features of the eigenvalue distribution in the absence and presence of noise are discussed using dipolar coupling data calculated from conformational ensembles taken from a molecular dynamics trajectory of native ubiquitin. [ABSTRACT FROM AUTHOR]

Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was calculated separately by the abinitiomolecular orbital method. All the calibrated potentials of mean forcecoincided well. The calibration was applied to a peptide in explicit water,and the calibrated free energy landscapes did not depend on the force fieldused in conformational sampling, as far as the conformational space waswell sampled. [ABSTRACT FROM AUTHOR]

Although techniques for the simulation of biomolecules, such as proteins and RNAs, have greatly advanced in the last decade, modeling complexes of biomolecules with metal ions remains problematic. Precise calculations can be done with quantum mechanical methods but these are prohibitive for systems the size of macromolecules. More qualitative modeling can be done with molecular mechanical potentials but the parametrization of force fields for metals is often difficult, particularly if the bonding between the metal and the groups in its coordination shell has significant covalent character. In this paper we present a method for deriving bond and bond-angle parameters for metal complexes from experimental bond and bond-angle distributions obtained from the Cambridge Structural Database. In conjunction with this method, we also introduce a non-standard energy term of gaussian form that allows us to obtain a stable description of the coordination about a metal center during a simulation. The method was evaluated on Fe(II)-porphyrin complexes, on simple Cu(II) ion complexes and a number of complexes of the Pb(II) ion. [ABSTRACT FROM AUTHOR]