Construction of molecular structure and active site analysis of Zichang coking coal: experimental and computational study.

In the study, the structural parameters of Zichang (ZC) coking coal from northern Shaanxi Province were examined. A theoretical calculation was employed to build a molecular structure model for ZC coal, as well as applying principles of quantum chemistry, the prediction of NMR spectrogram and density for the model was achieved, and the molecular chemical formula was C199H155O36N3. The molecular structure optimization and annealing kinetics calculations are based on molecular mechanics (MM) and molecular dynamics (MD). Subsequently, a representative simplified model was constructed using the aromatic structure as the fundamental unit. On this foundation, the electrostatic potential (ESP), atomic charge distribution, and energy level orbitals were analyzed for this simplified model. The outcomes of this research can serve as an essential guide for determining the reaction order of the active categories during the low-temperature oxidation process for ZC coking coal.

Study of starch molecular structure-property relations provides new insight into slowly digested rice development.

White rice consumption has been regarded as a potential risk factor for non-communicable diseases including obesity and type 2 diabetes. Thus, increasing attention has been paid to develop slowly digested rices with acceptable palatability. As the most abundant component of rice kernels, the fine molecular structure of starch controls not only the texture & aroma, but also the digestion properties of cooked rice. A large number of studies have been conducted to see what molecular structural features control the digestibility and palatability of cooked rice, which further could be connected to starch biosynthesis to enable rices with targeted functionalities to be chosen in non-empirical ways. Nonetheless, little progress has been made because of improper experimental designs. For example, the effects of starch fine molecular structure on cooked rice digestibility and palatability has been rarely studied within one study, resulting to various digestion results. Even for the same sample, it is hard to obtain consistent conclusions and sometimes, the results/coclusions are even controversy. In this review paper, starch fine molecular structural effects on the texture, aroma and starch digestion properties of cooked white rice were summarized followed by a detailed discussion of the relations between the fine molecular structures of amylopectin and amylose to deduce a more general conclusion of starch molecular structure-cooked rice property relations. It is expected that this review paper could provide useful information in terms of how to develop slowly digested rices with acceptable palatability.

Structural insights into transcription activation of the Streptomyces antibiotic regulatory protein, AfsR.

The Streptomyces antibiotic regulatory proteins (SARPs) are ubiquitously distributed transcription activators in Streptomyces and control antibiotics biosynthesis and morphological differentiation. However, the molecular mechanism behind SARP-dependent transcription initiation remains elusive. We here solve the cryo-EM structure of an AfsR-loading RNA polymerase (RNAP)-promoter intermediate complex (AfsR-RPi) including the Streptomyces coelicolor RNAP, a large SARP member AfsR, and its target promoter DNA that retains the upstream portion straight. The structure reveals that one dimeric N-terminal AfsR-SARP domain (AfsR-SARP) specifically engages with the same face of the AfsR-binding sites by the conserved DNA-binding domains (DBDs), replacing σHrdBR4 to bind the suboptimal -35 element, and shortens the spacer between the -10 and -35 elements. Notably, the AfsR-SARPs also recruit RNAP through extensively interacting with its conserved domains (ß flap, σHrdBR4, and αCTD). Thus, these macromolecular snapshots support a general model and provide valuable clues for SARP-dependent transcription activation in Streptomyces.

Intermolecular Interactions between Aldehydes and Alcohols: Conformational Equilibrium and Rotational Spectra of Acrolein-Methanol Complex.

The rotational spectra of the 1:1 complex formed by acrolein and methanol and its deuterated isotopologues have been analyzed. Two stable conformations in which two hydrogen bonds between the two moieties are formed were detected. The rotational lines show a hyperfine structure due to the methyl group internal rotation in the complex and the V3 barriers hindering the motion were determined as 2.629(5) kJ mol-1 and 2.722(5) kJ mol-1 for the two conformations, respectively. Quantum mechanical calculations at the MP2/aug-cc-pVTZ level and comprehensive analysis of the intermolecular interactions, utilizing NCI and SAPT approaches, highlight the driving forces of the interactions and allow the determination of the binding energies of complex formation.

Investigation of the link between first-order kinetic models of the in vitro digestion of native starches and the accompanying changes in their crystallinity and structure.

Starch is the main source of dietary energy for humans. In order to understand the mechanisms governing native starch in vitro digestion, digestion data for six starches [wheat, maize, (waxy) maize, rice, potato and pea] of different botanical sources were fitted with the most common first-order kinetic models, i.e. the single, sequential, parallel and combined models. Parallel and combined models provided the most accurate fits and showed that all starches studied except potato starch followed a biphasic in vitro digestion pattern. The biological relevance of the kinetic parameters was explored by determining changes in crystallinity and molecular structure of the undigested starch residues during in vitro digestion. While the crystallinity of the undigested potato starch residues did not change substantially, a respectively small and large decrease in their amylose content and chain length during in vitro digestion was observed, indicating that amylose was digested slightly preferentially over amylopectin in native starch. However, the molecular structure of the starch residues changed too slowly and/or only to an insufficient extent to relate it to the kinetic parameters of the digested fractions predicted by the models. Such parameters thus need to be interpreted with caution, as their biological relevance still needs to be proven.

Extrusion can ameliorate negative effects of molecular structures of brewer's spent grain on energy contents and amino acid digestibility in growing pigs.

The objectives of this study were to investigate the effects of extrusion on the chemical compositions, surface structure, and molecular structure of brewer's spent grain (BSG), as well as to determine the digestible energy (DE), metabolizable energy (ME), apparent total tract digestibility (ATTD) of nutrients and energy, and amino acid (AA) digestibility of extruded BSG when fed to growing pigs. Firstly, we determined the changes in chemical compositions and molecular structure of both non-extruded and extruded BSG. In Exp. 1, eighteen growing pigs were fed three different diets including one corn-soybean meal basal diet and two experimental diets containing 20% BSG with or without extrusion. Feces and urine were collected to determine the ATTD of nutrients and energy, DE, and ME of extruded or non-extruded BSG. In Exp. 2, eighteen growing pigs were fed three different diets including 30% BSG with or without extrusion, and an N-free diet. Ileal digesta was collected through the slaughter method to determine the apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of AA of extruded or non-extruded BSG. The results showed that extrusion reduced the neutral detergent fiber, hemicellulose and cellulose contents in BSG, and increased the Arg, Asp, Glu, Ser, Tyr, total indispensable AA and total AA contents of BSG, altered the surface structure of BSG, increased the peak absorbance in amide I and amide II height, amide II and amide (I+II) area, α-helix height, decreased ß-sheet height, and weakened band intensities in cellulosic compounds (CELC) area, structural carbohydrates (SCHO) area, carbohydrates area (CHO) peak 2 and 3 height, the area ratio of CELC: CHO and CELC: SCHO. Moreover, DE and ME values and ATTD of energy, dry matter, crude protein, acid detergent fiber, neutral detergent fiber, cellulose and hemicellulose increased (P < 0.05) when pigs were fed extruded BSG diets. The AID and SID of Arg, His, Lys, Val and Gly increased, whereas the AID and SID of Ile and Leu decreased when pigs were fed extrusion diets (P < 0.05). Our study found that the ATTD of nutrients and AA digestibility in pigs were positively correlated with the molecular structure of proteins, and negatively correlated with the molecular structure of carbohydrates (P < 0.05). These findings suggested that extrusion had the potential to improve the nutrient digestibility of BSG by altering its chemical compositions, surface structure, and molecular structure.

Computation of differential and integral operators using M -polynomials of gold crystal.

Gold is generally considered a noble metal since it is inherently inert in its bulk state. However, gold demonstrates reactivity when it is in its ionic state. The inherent inertness of bulk gold has resulted in its widespread recognition as a vital raw material in various biomedical processes. The applications of these technologies include drug delivery microchips, dental prostheses, reconstructive surgery, culinary additives, and cardiovascular stents. Gold can also exist in molecules or ions, particularly gold ions, which facilitates the production of gold nanomaterials. In this paper, we have computed differential and integral operators by using the M -Polynomial of gold crystals and by utilizing this polynomial, we have also computed eleven topological indices like 1 s t Zagreb, 2 n d Zagreb, Hyper, Sigma, Second Modified, General Randic, General Reciprocal Randic, 3 r d Redefined Zagreb, Symmetric Division Degree, Harmonic, Inverse Sum indices for the structure of Gold crystal.

Degree-based topological indices and entropies of diamond crystals.

High hardness, low friction coefficient and chemical resistance are only a few of the exceptional mechanical qualities of diamond. Diamonds can be artificially created to have different levels of conductivity, or they can be single, micro or nanocrystalline and highly electrically insulating. It also has high biocompatibility and is famous for being mechanically robust. Due to its high hardness, lack of ductility and difficulty in welding, diamond is a challenging material to construct devices with. Diamonds have experienced a rise in attention as a biological material in recent decades due to new synthesis and fabrication techniques that have eliminated some of these disadvantages. In general, entropic measurements are used for investigating the chemical or biological properties of molecular structures. This study calculates several important K-Banhatti entropies, redefined Zagreb entropies and atom-bond sum connectivity entropy for diamond crystals. We also present a numeric and graphical explanations of obtain indices.

Impact of sugar and sugar alcohol on the pasting and retrogradation properties of starch with distinct molecular structures.

The molecular structures of starch and sugar/sugar alcohol are recognized as critical determinants of starch pasting and retrogradation properties. However, their combined effects on these properties remain elusive. This study for the first time examined the pasting and retrogradation properties of nine starches with diverse molecular structures, both with and without the addition of glucose, sucrose, isomaltose, isomalt, and sorbitol. The presence of sugar/sugar alcohol significantly enhanced starch pasting viscosity. In particular, the variations of the peak viscosity of wheat starch were more pronounced than other starches, possibly due to its distinct molecular structures. The changes in melting temperatures and enthalpy of retrograded starches were complex, varying depending on the type of starch and sugar/sugar alcohol used. For example, the melting peak temperature ranged from 56.45 °C (TS) to 61.9 °C (WMS), and the melting enthalpy ranged from 0.16 J/g (TS) to 5.6 J/g (PES). The micromorphology of retrograded starch revealed agglomeration and needle-like structures, instead of a network structure, after the addition of glucose and sorbitol, respectively. Correlations between starch molecular structure and pasting properties remained largely unchanged, while the relationship between starch molecular structure and retrogradation properties exhibited notable variations after the addition of sugars or sugar alcohols. These findings help a better understanding of the effects of starch molecular structure and the presence of sugar/sugar alcohol on starch pasting and retrogradation properties.

Insights into structural vaccinology harnessed for universal coronavirus vaccine development.

Structural vaccinology is pivotal in expediting vaccine design through high-throughput screening of immunogenic antigens. Leveraging the structural and functional characteristics of antigens and immune cell receptors, this approach employs protein structural comparison to identify conserved patterns in key pathogenic components. Molecular modeling techniques, including homology modeling and molecular docking, analyze specific three-dimensional (3D) structures and protein interactions and offer valuable insights into the 3D interactions and binding affinity between vaccine candidates and target proteins. In this review, we delve into the utilization of various immunoinformatics and molecular modeling tools to streamline the development of broad-protective vaccines against coronavirus disease 2019 variants. Structural vaccinology significantly enhances our understanding of molecular interactions between hosts and pathogens. By accelerating the pace of developing effective and targeted vaccines, particularly against the rapidly mutating severe acute respiratory syndrome coronavirus 2 and other prevalent infectious diseases, this approach stands at the forefront of advancing immunization strategies. The combination of computational techniques and structural insights not only facilitates the identification of potential vaccine candidates but also contributes to the rational design of vaccines, fostering a more efficient and targeted approach to combatting infectious diseases.

High sulphur oil of Type II kerogen of the oil shales from Western Central Jordan based on molecular structure and kinetics.

Organic rich sedimentary rocks of the Late Cretaceous Muwaqqar Formation from the Lajjun outcrop in the Lajjun Sub-basin, Western Central Jordan were geochemically analyzed. This study integrates kerogen microscopy of the isolated kerogen from 10 oil shale samples with a new finding from unconventional geochemical methods [i.e., ultimate elemental (CHNS), fourier transform infrared spectroscopy and pyrolysis-gas chromatography (Py-GC)] to decipher the molecular structure of the analyzed isolated kerogen fraction and evaluate the kerogen composition and characteristics. The optical kerogen microscopy shows that the isolated kerogen from the studied oil shales is originated from marine assemblages [i.e., algae, bituminite and fluorescence amorphous organic matter] with minor amounts of plant origin organic matter (i.e., spores). This finding suggests that the studied kerogen is hydrogen-rich kerogen, and has the potential to generate high paraffinic oil with low wax content. The dominance of such hydrogen-rich kerogen (mainly Type II) was confirmed from the multi-geochemical ratios, including high hydrogen/carbon atomic of more than 1.30 and high A-factor of more than 0.60. This claim agrees with the molecular structure of the kerogen derived from Py-GC results, which suggest that the studied kerogen is mainly Type II-S kerogen exhibiting the possibility of producing high sulphur oils during earlier stages of diagenesis, according to bulk kinetic modeling. The kinetic models of the isolated kerogen fraction suggest that the kerogen conversion, in coincidence with a vitrinite reflectance range of 0.55-0.60%, commenced at considerably lower temperature value ranges between 100 and 106 °C, which have produced oils during the early stage of oil generation. The kinetic models also suggest that the commercial amounts of oil can generate by kerogen conversion of up to 50% during the peak stage of oil window (0.71-0.83%) at relatively low geological temperature values in the range of 122-138 °C. Therefore, further development of the Muwaqqar oil shale successions is highly approved in the shallowly buried stratigraphic succession in the Lajjun Sub-basin, Western Central Jordan.

Effects of calcium ions and polysaccharides type on transparent exopolymer particle formation and the related fouling mechanisms.

Organics and divalent cations are the primary barriers constraining the performance of membrane technology, while the interactions between them and the detailed mechanisms of their impacts are still lacking in-depth analysis. In this study, sodium alginate and xanthan gum were selected as polysaccharides models, and the formation of transparent extracellular polymer particles (TEP) was assessed to examine the effect of Ca2+ and polysaccharides type on membrane fouling from both qualitative and quantitative perspectives. The results revealed that higher Ca2+ concentrations led to a greater abundance of TEP, and the transformation of TEP microstructure is a key factor for the membrane fouling change indicated by specific filtration resistance (SFR). TEP formed by sodium alginate underwent a transformation from amorphous-TEP (a-TEP) form to particle-TEP (p-TEP), corresponding to a unimodal pattern of SFR variation. With increasing Ca2+ concentration, the molecular interactions of xanthan gum became stronger, resulting in larger fibrous a-TEP and a continuous SFR increase. According to the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, TEP formed by xanthan gum exhibited higher adhesion energy, thus causing more severe membrane fouling. The SFR variation of the TEP system can be satisfactorily explained by the conception of chemical potential change in the filtration process depicted in Flory-Huggins theory. This study is the first work to introduce models regarding chemical potential and TEP microstructure, linking the system chemical potential and TEP microstructure with membrane fouling indicated by SFR. As all, this study provided a new perspective for analyzing the polysaccharide fouling behavior via TEP determination and further enhanced the understanding through thermodynamic analysis.

Cytochrome c prompts the recruitment of its nuclear partners SET/TAF-Iß and NPM1 into biomolecular condensates.

Compartmentalization of proteins by liquid-liquid phase separation (LLPS) is used by cells to control biochemical reactions spatially and temporally. Among them, the recruitment of proteins to DNA foci and nucleolar trafficking occur by biomolecular condensation. Within this frame, the oncoprotein SET/TAF-Iß plays a key role in both chromatin remodeling and DNA damage response, as does nucleophosmin (NPM1) which indeed participates in nucleolar ribosome synthesis. Whereas phase separation by NPM1 is widely characterized, little is known about that undergone by SET/TAF-Iß. Here, we show that SET/TAF-Iß experiences phase separation together with respiratory cytochrome c (Cc), which translocates to the nucleus upon DNA damage. Here we report the molecular mechanisms governing Cc-induced phase separation of SET/TAF-Iß and NPM1, where two lysine-rich clusters of Cc are essential to recognize molecular surfaces on both partners in a specific and coordinated manner. Cc thus emerges as a small, globular protein with sequence-encoded heterotypic phase-separation properties.

Exploring the conformational landscape through rotational spectroscopy and computational modelling: The tunneling dynamics in 2,6-diethylphenol.

Phenol and some of its derivatives exhibit interesting tunneling motions consisting of two groups of transitions separated by a few hundred MHz. Recently, one of its derivatives, 2,6-di-tert-butylphenol, has shown additional hyperfine tunneling components, the origin of which remains unclear. In this work, another member of the family, 2,6-diethylphenol, has been investigated through its rotational spectrum. The jet-cooled broadband chirped-pulse Fourier transform microwave spectra in the 2-8 GHz frequency region revealed the presence of two conformers. The comparison with the equilibrium structure obtained by computational calculations at the B3LYP-D3(BJ)/Def2-TZVP level validates the structural determination and the orientation of the lateral ethyl groups. Additional observation of all the singly-substituted 13C isotopologues for the most stable ones allowed the determination of the substitution structure by means of the Kraitchman equations. Both conformers exhibited tunneling that was reproduced using an advanced 1D model, which provides an estimate of the barrier height for both conformers.

Impact of fermentation by Saccharomyces Cerevisiae on the macronutrient and in vitro digestion characteristics of Chinese noodles.

This study examined the impact of live bread yeast (Saccharomyces cerevisiae) on the nutritional characteristics of Asian dried noodles. Micronutrient analysis of fermented noodles revealed a 6.9% increase in the overall amino acid content, a 37.1% increase in the vitamin B content and a 63.0% decrease in the phytic acid level. Molecular weight analysis of starch and protein contents revealed moderate decrease in the fermented noodles. The in vitro digestion of fermented noodles showed a slightly faster initial acidification, four-fold decrease in the initial shear viscosity (from 8.85 to 1.94 Pa·s). The initial large food particle count (>2 mm diameter) was 19.5% lower in the fermented noodles. The fermented noodles contained slightly higher free sugar content (73.5 mg g-1 noodle) during the gastric digestion phase. The overall nutrition and digestion results indicate nutritional improvement and digestion-easing attributes in the fermented noodles.

Multiple drivers and mechanisms of solid-water interfacial interactions in sludge dewatering: Roles of polarity and molecular structure of extracellular polymeric substances.

Water occurrence states in sewage sludge, influenced by sludge physicochemical properties, are crucial for sludge dewaterability and have recently been regarded as a research hotspot. Here, the multifold characteristics of sludge flocs during hydrothermal treatment, including rheological properties, solid-water interfacial interactions, and the polarity distribution and molecular structure of extracellular polymeric substances (EPS), were systematically investigated, and the impact of these characteristics on sludge dewaterability was explored in depth. Hydrothermal treatment at 80 °C and 100 °C induced the conversion of free water into bound water, while an increase in temperature to 180 °C resulted in a significant decrease in bound water content, approximately 4-fold lower than at 100 °C. In addition to the conventional view of decreased sludge surface hydrophilicity at high temperatures, the decline in bound water was associated with the reduction in sludge apparent viscosity. XAD resin fractionation identified the hydrophobic/hydrophilic EPS (HPO-/HPI) ratio as an important factor determining water occurrence states. Especially, hydrolysis of HPI-related hydrophilic proteins and subsequent increase in HPO-related tryptophan-like substances played a dominant role in reducing sludge viscosity and facilitating the release of bound water. Protein conformational analysis revealed that the disruption of α-helix structures and disulfide bonds significantly reduced EPS water-holding capacity, providing strong evidence for the potential of targeting these dense structure units to enhance sludge dewaterability. These findings provide a holistic understanding of multidimensional drivers of water occurrence states in sludge, and guide directions for optimizing sludge treatment efficiency through EPS modification.

Rheological, textural, and pasting properties of A- and B-type wheat starches in relation to their molecular structures.

A- and B-type wheat starches have significant differences in rheological, textural, and pasting properties; however, the structure-property relationship is not fully revealed. Herein, the physicochemical characteristics and molecular structures of A- and B-type starches isolated from three wheat varieties with different apparent amylose contents (2.41%-27.93%) were investigated. A-type starches exhibited higher pasting viscosities, relative crystallinity, onset gelatinization temperatures, and enthalpies, while B-type starches had wide gelatinization temperature ranges. B-type starches had lower resistant starch contents than their A-type counterparts, but B-type starches formed more stable gels and had a lower tendency to retrograde, resulting in lower hardness, storage (G') and loss (G'') moduli but higher tan δ values. A-type starches had lower contents of short amylose (100 ≤ X < 1000) and amylopectin chains (DP 6-12) than B-type. These findings elucidated the differences in molecular structures between A- and B-type starches, which can contribute to their effective application.

A non-symmetrical p97 conformation initiates a multistep recruitment of Ufd1/Npl4.

In vitro experiments and cryo-EM structures of p97 and its cofactor, Ufd1/Npl4 (UN), elucidated substrate processing. Yet, the structural transitions and the related ATPase cycle upon UN binding remain unresolved. We captured two discrete conformations: One in which D1 protomers are ATP bound, while the D2 subunits are in the ADP state, presumably required for substrate engagement with the D2 pore; and a heterologous nucleotide state within the D1 ring in which only two NTDs are in the "up" ATP state that favors UN binding. Further analysis suggests that initially, UN binds p97's non-symmetrical conformation, this association promotes a structural transition upon which five NTDs shift to an "up" state and are poised to bind ATP. The UBXL domain of Npl4 was captured bound to an NTD in the ADP state, demonstrating a conformation that may provide directionality to incoming substrate and introduce the flexibility needed for substrate processing.

Development of CDK12 as a Cancer Therapeutic Target and Related Inhibitors.

Cyclin-dependent Kinase 12 (CDK12) is a Cyclin-dependent Kinase (CDK) that plays a crucial role in various biological processes, including transcription, translation, mRNA splicing, cell cycle regulation, and DNA damage repair. Dysregulation of CDK12 has been implicated in tumorigenesis, and genetic alterations affecting CDK12 have been identified in multiple cancer types, including breast cancer, ovarian cancer, gastric cancer, and prostate cancer. Numerous studies have demonstrated that suppression of CDK12 expression effectively inhibits tumor growth and proliferation, underscoring its significance as a cancer biomarker and a potential therapeutic target in cancer treatment. A thorough comprehension of CDK12 is expected to significantly enhance the advancement of novel approaches for the treatment and prevention of cancer. In recent times, endeavors have been undertaken to formulate targeted inhibitors for CDK12, such as PROTAC and molecular gel degraders. Concurrently, investigations have been conducted on the combined utilization of CDK12 small molecule inhibitors and immunotherapy as a potential strategy. This paper examines the diverse functions of CDK12 in the modulation of gene expression and its implications in human tumors. Specifically, it explores the recently uncovered roles of CDK12 kinases in various cellular processes, emphasizing the potential of CDK12 as a viable therapeutic target for the management of human tumors. Furthermore, this review provides an up-to-- date account of the advancements made in utilizing CDK12 in tumor therapy.

Dystrophic epidermolysis bullosa characterized by mucosal lesions in a Chinese familial case with a novel compound heterozygous mutation of COL7A1.

Dystrophic epidermolysis bullosa (DEB) is a rare, but severe, subtype of epidermolysis bullosa. It is characterized mainly by blisters and miliary rashes of the skin, while oral mucosa-dominated cases are extremely rare. Here, we report the characteristics of oral mucosa lesions in a Chinese familial case of DEB with a novel compound heterozygous COL7A1 mutation. We further analyzed the genetic and molecular features of the proband and the two related mutation carriers. Our study further elucidates the genetic and phenotypic heterogeneity of DEB.