Secondary Structure Distribution Research Articles

Reverse Micelles Extraction of Prolamin from Baijiu Jiuzao: Impact of Isolation Process on Protein Structure and Morphology.

Prolamins, proteins derived from plants, have extensive applications in pharmaceutics and food science. Jiuzao is a byproduct of the Baijiu brewing industry, and is a great source of prolamin. Despite its importance, knowledge regarding the extraction techniques and the properties of prolamin derived from Baijiu Jiuzao (PBJ) remains limited. Reverse micelles (RMs) extraction offers an efficient and cost-effective method for purifying proteins. In the present study, prolamin was extracted from Baijiu Jiuzao using RMs extraction and subsequently characterized in terms of its secondary structure, morphology, and particle size distribution. Our findings indicate that the purified prolamin extracted using further RMs extraction possessed higher α-helix content (+13.25%), forming a large-scale protein network, and narrower particle size distributions compared to the crude prolamin obtained by NaOH-ethanol method. This research suggests that RMs extraction has potential applications in extracting prolamin from brewing industry byproducts, offering an environmentally friendly approach to Baijiu Jiuzao recycling.

Excellent hydrophobicity and high mobility of condensate droplets on hierarchical nanostructured surfaces: Insights from MD simulations

Comprehending the fundamental physical mechanisms behind condensation and the formation of suspended droplets on hierarchical structured surfaces is of paramount importance in the design of anti-frosting surfaces. In this study, we characterize the nucleation, growth and dynamic wetting behaviors of condensate droplets on hierarchical nanostructured surfaces by molecular dynamics simulation, and reveal that hierarchical structures facilitate the rapid formation and high mobility of suspended droplet during condensation. The mechanism underlying the formation of suspended droplets on hierarchical surfaces is unveiled, which can be attributed to the spontaneous dewetting transition induced by confined growth of individual droplets. Additionally, the impact of solid fraction and secondary structure distribution on condensation and dynamic wetting is systematically discussed. The results indicate that an increase in solid fraction or the number of secondary structures enhances the stability of suspended droplets and improves the droplet mobility. In particular, the presence of bottom secondary structures on sidewalls plays a crucial role in the formation of suspended droplets on hierarchical surface. It is expected that the above findings could provide valuable guidance for optimizing the design of functionalized surfaces with anti-frosting and self-cleaning performance.

An interpretable deep learning model predicts RNA–small molecule binding sites

The intricate interplay between RNA molecules and small ligands plays a pivotal role in regulating biological processes, underscoring the necessity for accurate prediction models of RNA–small molecule binding sites. In this study, we develop CapBind, a novel interpretive deep learning framework utilizing a Capsule Network architecture, to precisely identify RNA–small molecule binding sites. This framework stands out for its multifaceted approach, which leverages both the sequence and structural information of RNA as input features, allowing for a thorough understanding of the complex interactions between RNA and small molecules. Leveraging multi-source bioinformatics data, including the distribution of RNA secondary structures, our model characterizes sequence and structural features with unparalleled depth. Through a unified alignment of these multi-source feature representations, we achieve dimensional homogeneity in the potential feature maps for both types of biological data. The crux of our methodology lies in the deployment of a multi-level Capsule Network, engineered to identify the nuanced interactions of RNA sequences with small molecules. The essence of our approach resides in the implementation of a multi-layered Capsule Network. Utilizing a sophisticated routing mechanism, this network demonstrates unparalleled efficacy in learning and identifying the intricate interactions between RNA sequences and small molecules. This mechanism enables dynamic adjustment of information flow across multiple levels, thereby capturing subtle features and patterns that might elude conventional neural network architectures. The experimental results demonstrate the superior performance of our model, particularly highlighting its progress in evaluation metrics compared to current state-of-the-art models. Case studies further validate the model’s precision in identifying binding sites, offering potential insights into gene expression pathways and novel therapeutic avenues for neurodegenerative diseases. Moreover, an extensive interpretability analysis of our silicon model reveals the internal interaction mechanisms between specific RNA regions and small molecules, contributing valuable perspectives for drug design and molecular biology research. These findings underscore the model’s predictive accuracy and biological applicability, establishing our approach as a significant leap forward in the computational prediction of RNA–small molecule binding sites.

Mechanical properties of hierarchical lattice via strain gradient homogenization approach

With the advancement of 3D printing technology, manufacturing metamaterials with extreme mechanical properties is becoming more feasible. Hierarchical lattices appear to be ideal candidates for obtaining desirable lightweight, high specific stiffness, and enhanced specific energy absorption. They can be constructed by architected substructures at multiple length scales. The interpretations of the underlying deformation mechanisms are necessary in order to manipulate with expected mechanical properties. In this paper, experiments were conducted to examine the effective mechanical behaviors of hierarchical lattice metamaterials. A strain gradient homogenization approach has been employed to correlate their morphological characteristics to the resulting material properties. The effective stiffness tensors are identified including the fourth-, fifth-, and sixth-order stiffness tensors. The higher-order inertial parameters are determined by a fitting procedure. Comparisons between direct finite element analyses and the homogenized strain gradient continua have been made for hierarchical lattice materials under static and dynamic loads. It is found that strain gradient homogenization approach can be an accurate, efficient and reliable way of predicting the mechanical behaviors of hierarchical lattice. A systematic analysis of geometrical parameters was conducted to uncover the underlying mechanisms responsible for the enhancement of effective properties. This work offers a novel approach for designing the mechanical properties of hierarchical metamaterials through precise control of secondary structure types and distributions.

A structure‐based fluid biomarker for the differential diagnosis of early‐stage neurodegenerative diseases measured by the immuno‐infrared‐sensor (iRS)

AbstractBackgroundNeurodegenerative diseases like Alzheimer’s (AD) and Parkinson’s disease (PD) are accompanied by misfolding of the key proteins into beta‐sheet enriched structures resulting in high neurotoxicity in early phases. We have developed a diagnostic immuno‐infrared‐sensor (iRS) that monitors the secondary structure distribution of these key proteins (Abeta for AD, alpha‐synuclein for PD) as an early detectable biomarker before the clinical manifestation, which is shown exemplarily for AD.1 MethodThe iRS combines the secondary‐structure‐specific infrared spectroscopy in a flow system based attenuated total reflection (ATR) set‐up with methods of immuno‐detection by surface‐immobilized antibodies. The antibodies specifically capture disease‐related target proteins (e.g., Abeta) from complex media (cerebrospinal fluid or blood plasma) for measurements. The readout is the amide‐I band, which directly reflects the secondary structure distribution of the captured proteins in body fluids and thus, indicates the protein misfolding: The lower the amide‐I frequency, the higher the content of misfolded Abeta species in the sample present.2 ResultThe structure biomarker for Abeta has been validated in multiple independent clinical studies with strong correlation to CSF biomarkers and PET scans.1,3‐5 Especially, very early preclinical AD could be identified in symptom‐free individuals before plaque formation, up to 17 years before the diagnosis.6 ConclusionThe results demonstrate a highly specific and sensitive immune‐assay capable of tracking structural changes of Abeta before clinical manifestation of AD. In addition, alpha‐synuclein and TDP‐43 misfolding indicate PD and ALS in current discovery studies, providing a tool for differential diagnosis at early stages.

Rational Design of a Biocatalyst Based on Immobilized CALB onto Nanostructured SiO2

The adsorption of the lipase B from Candida antarctica (CALB) over nanostructured SiO2 (Ns SiO2 from now on) with and without the addition of polyols (sorbitol and glycerol) was investigated. The isotherms of adsorption made it possible to establish that the maximum dispersion limit was 0.029 µmol of protein per surface area unit of Ns SiO2 (29.4 mg per 100 mg of support), which was reached in 30 min of exposure. The studies through SDS-PAGE of the immobilization solutions and infrared spectroscopy of the prepared solids determined that CALB (from a commercial extract) is selectively adsorbed, and its secondary structure distribution is thus modified. Its biocatalytic activity was corroborated through the kinetic resolution of rac-ibuprofen. Conversions of up to 70% and 52% enantiomeric excess toward S-ibuprofen in 24 h of reaction at 45 °C were achieved. The biocatalytic performance increased with the increase in protein loading until it leveled off at 0.021 µmol.m−2, reaching 0.6 µmol.min−1. The biocatalyst containing the lipase at the maximum dispersion limit and co-adsorbed polyols presented the best catalytic performance in the kinetic resolution of rac-ibuprofen, an improved thermal resistance (up to 70 °C), and stability under long-term storage (more than 2 years).

Insight into Antioxidant Activity and Peptide Profile of Jinhua Ham Broth Peptides at Different Cooking Times.

This present study aimed to investigate the effects of various cooking times (1 h, 1.5 h, 2 h, 2.5 h, named as JHBP-1, JHBP-1.5, JHBP-2, JHBP-2.5) on the antioxidant activity and peptide profile of Jinhua ham broth peptides (JHBP). The peptides extracted from uncooked ham were used as an uncooked group with the name of JHBP-0. The results revealed that the antioxidant efficacy in the four cooked groups changed dramatically compared to JHBP-0. After cooking, the DPPH radical scavenging activity, hydroxyl radical scavenging activity and superoxide anion radical scavenging activity decreased, except for the Fe2+ chelation and ABTS+ scavenging capacity which increased significantly. However, the cooked groups still showed a strong antioxidant capacity. In particular, the superoxide anion radical scavenging ability and the Fe2+ chelation action were significantly stronger compared to glutathione (GSH) and butylated hydroxytoluene (BHT) (p < 0.05). JHBP-1.5 also displayed stronger antioxidant capacity than the other three cooked groups, and its secondary structure and mass distribution changed significantly after cooking, specifically with an increased proportion of helix and <1 kDa peptides. Moreover, the constitution of free amino acids (FAAs) and the types of peptides released in the broth increased significantly with a longer cooking time. In total, 1306 (JHBP-0), 1352 (JHBP-1), 1431 (JHBP-1.5), 1500 (JHBP-2), and 1556 (JHBP-2.5) peptide sequences were detected using LC-MC/MC. The proportion of <1 kDa peptides also gradually increased as the cooking time extended, which is consistent with the molecular weight distribution measurements.

Dipole Cooperativity and Polarization Frustration Determine the Secondary Structure Distribution of Short Alanine Peptides in Water.

The physical driving forces for secondary structure preferences of hydrated alanine peptide are investigated with B3LYP-D3(BJ) and the adaptive force matching (AFM) method. The AFM fit to the DFT surface, ALA2022, provides excellent agreement with the nuclear magnetic resonance scalar coupling constants from experiments. In turn, the model is used to gain insight into the physical driving forces behind secondary structure preferences of hydrated peptides. DFT calculations with and without the Conductor-like Screening Model (COSMO) show that the α helix is stabilized by solvent polarization due to dipole cooperativity. The two adjacent amide groups in β strand form a near-planar trapezoid that is not much larger than the size of water molecules. When the finite size of a water molecule is considered, the stabilization from solvent polarization for such a trapezoid is frustrated. Water molecules cannot find orientations to properly stabilize all four polar regions close to each other with such an awkward arrangement. This leads to quite substantial reduction in polarization stabilization. Although the polyproline II (PP-II) conformation is very similar to the β strand, the small twist in the backbone angles allowed much improved polarization stabilization. The improved polarization, when combined with favorable intrapeptide interactions, leads to the PP-II to be lowest in free energy. Other factors, such as the entropic TΔS and the ϕ, ψ coupling terms, are also studied but are found to play only a minor role. The insight shown in this work helps to better understand the structure of globular and intrinsic disordered proteins and facilitate future force field development.

Using Maxwell’s Theory to model and quantify the fracture evolution of cyclothymic deposition phosphate rock

The evolution and stability of fracturing in the cyclothymic deposition of phosphate rocks are strongly affected by the viscoelasticity and structural form of the rock-forming minerals. Presently, there is no standardized method that has been widely accepted to accurately quantify the elastic-plastic deformation and fracturing of such striped structural rock nor reflect the role of the different lithogenous minerals in phosphate rocks when subjected to viscoelastic strain loading. In this study, integrated mathematical equations were formulated for modelling the mechanical and fracture behaviour of cyclothymic deposition in structured phosphate rocks. These constitutive equations were developed based on Maxwell’s Theory after the elastic modulus and damping coefficient of the rock-forming mineral from the mechanical testing were substituted into the derived-equations. In these new models, the apatite stripes and dolomite stripes were incorporated into the transverse isotropic model through the analysis of structural characteristics of the phosphate rock. Through experimental validation, the response curves of the creep and stress relaxation tests were found to be consistent with the deformation curves generated by modelling using the mathematical equations. Overall, the formulated model along with the corresponding equations was found to exhibit good applicability properties to describe phosphate’s mechanical and fracture behaviour under low horizontal compressive stresses. In the study, the creep mechanism in phosphate rocks were satisfactorily analysed from the angles of microscopic morphology, cracks evolution, and inter-crystalline strength. The hard brittle apatite was found to be surrounded and separated by high creep variant dolomite. Furthermore, the analysis showed that dolomite crystals possessing high creep properties dominated the distribution and evolution of secondary structures in the phosphate rock, under the condition of long-term low-stress loading.

The amino acids differences in epitopes may promote the different allergenicity of ovomucoid derived from hen eggs and quail eggs

Quail egg ovomucoid can inhibit activation of basophils and eosinophils, while hen egg ovomucoid has been shown to be a major allergen, named Gal d 1. At present, the differences in structure and function between two ovomucoid are unclear. We found the homology of ovomucoid in quail eggs and hen eggs reached 77 %. Compared with hen egg ovomucoid, the distribution of secondary structure was different in AA52−53, AA57−58, AA66−68, AA71−72, AA131−133, AA139−140, AA157−159 and AA184−185. Among 9 epitopes of egg ovomucoid, there were different amino acids from quail egg ovomucoid in 8 epitopes. Recombination quail egg ovomucoid had trypsin inhibition activity and quail egg ovomucoid didn’t specifically bind to serum of eggs allergic patients. Quail egg ovomucoid can significantly inhibit RBL-2H3 cells degranulation and protect cells morphology to a certain extent, indicating quail egg ovomucoid can inhibit cells activation and have potential anti-allergic effects, which is related to trypsin inhibitory activity. The difference in sensitization compare to hen egg ovomucoid may be due to amino acids differences affecting protein structure by changing antigenic epitopes.

Long QT syndrome-associated calmodulin mutations and their interactions with the Kv7.1 voltage-gated potassium channel

Abstract Introduction Calmodulin (CaM) is a highly conserved mediator of calcium (Ca2+) dependent signalling. Its flexible structure allows CaM to bind and modulate many targets, including cardiac ion channels. Genotyping has revealed several CaM mutations associated with congenital disorders of heart rhythm, known as long QT-syndrome (LQTS). LQTS patients suffer from prolonged ventricular recovery times (QT-interval) which increases their risk of significant cardiac events. Loss of function KV7.1 mutations are the largest cause of LQTS, accounting for &amp;gt;50% of cases. CaM facilitates Ca2+-sensitivity to KV7.1 in producing IKs, Kv7.1 mutations which reduce CaM binding promote LQTS pathology. However, the effects of LQTS-associated CaM mutations on Kv7.1 function remain unknown. Purpose To determine the biophysical consequences of congenital LQTS-associated CaM mutations and how they alter modulation of Kv7.1 in producing the ventricular repolarising IKs current. Methods WT and mutant CaM proteins were recombinantly expressed and purified for biophysical characterisation. Using circular dichroism, secondary structures and thermostability of proteins were quantified. Isothermal titration calorimetry was used to quantitatively measure interactions between CaM proteins and binding sites of KV7.1 (Helix B). NMR was employed to study the conformations of target-bound WT and mutant proteins. Whole cell currents were determined using voltage clamp electrophysiology in HEK cells. Results Mutations significantly changed the thermostability and secondary structure distributions of CaM, and also caused site-dependent increases in susceptibility to protease digestion. CaM interacted with Helix B (KV7.1) via both Ca2+-dependent and independent mechanisms. Ca2+ dependent binding to Helix B was much higher affinity than Ca2+-independent binding, with &amp;gt;2000-fold reduction in dissociation constant measured. LQTS-CaM variants reduced Helix B affinity with the largest reductions found in EF-hand IV mutants. These mutants also adopted most distinct conformations when Helix B-bound. Calmodulation of the KV7.1 channel produced larger (IKs) currents without altering channel activation kinetics. IKs exhibited Ca2+-sensitivity, in response to increased cytosolic Ca2+, larger currents were generated. Modulation by CaM mutants reduced current density at systolic Ca2+-concentrations (1000 nM), within physiological time periods (0.35 s), revealing a direct QT-prolonging modulatory effect. Conclusions Provided here are mechanistic insights as to how LQTS-associated CaM variants contribute to electrical disease of the heart. Mutations in the highly conserved structure of CaM disrupt protein conformation and perturb complex formation with KV7.1. This results in aberrant Ca2+-sensitivity of Kv7.1, reducing IKs generation. This ultimately decreases the repolarisation capacity of cells and would extend the QT interval of myocytes. Funding Acknowledgement Type of funding sources: Foundation. Main funding source(s): British Heart Foundation Intermediate Basic Science Research Fellowship

Direct current magnetic field: An optional strategy for reducing pyrophosphate in gelatinous meat products

This study was to investigate effects of direct-current magnetic field (DC-MF) and tetrasodium-pyrophosphate (TSPP) on properties of myofibrillar protein (MP) gels, to understand potential mechanisms of action, and to clarify feasibility of TSPP reduction by applying DC-MF. MP was either untreated or treated with DC-MF (9.5 mT) and TSPP (0–5 g/L) for 3 h, and then heat-induced gel was prepared for further analysis. Secondary structure, microstructure and water distribution of MP gels were measured respectively by Raman spectroscopy, scanning-electron-microscopy and low field NMR. The relationship between gel properties and protein structure was visualized by PCA. WHC obviously increased, while hardness, fracture and apparent viscosity became lower under DC-MF and high-level TSPP, with more significant effect on WHC, hardness and fracture as TSPP level changed than DC-MF. The texture of gels treated by DC-MF and 3 g/L TSPP was indistinguishable from that of 5 g/L control, delightfully, with TSPP usage decreasing from 5 to 3 g/L. DC-MF and TSPP could affect MP gel hydration ability by influencing microstructure, the content of α-helix and β-sheet, and exposing side-chain-residues. Gel texture was strongly correlated with random coil and β-turn. Overall, DC-MF and TSPP affected gel properties by altering protein and gel structure, DC-MF might be considered an optional strategy for reducing pyrophosphate in gelatinous meat products.

Study on moisture migration mechanism of dough during subfreezing storage

AbstractBackground and ObjectivesThe objective of this study was to investigate the effects of subfreezing storage on gluten protein denaturation and water retention. On this basis, the surface hydrophobicity, secondary structure, thermal stability, microstructure, and moisture distribution of gluten protein were measured.FindingsThe results showed that at the end of storage, the hydrophobicity indexes of wheat gluten proteins (−9°C and −12°C) stored under subfreezing conditions were significantly lower than those stored at 4°C and slightly lower than those stored at −18°C. The secondary structure stability of wheat gluten stored at −18°C was similar. P21 stored at −18°C was significantly higher than those stored at 4°C and showed an upward trend. The quality of the dough was similar to those stored at −18°C.ConclusionsThe deformation and water retention of gluten during subfreezing storage are similar to those stored at −18°C.Significance and NoveltyThe changes in dough moisture and gluten protein structure during frozen storage at different freezing temperatures were explored to provide a theoretical basis for the application of subfrozen storage in the frozen flour products industry.

Mechanical performance of bio-inspired hierarchical honeycomb metamaterials

Natural materials with hierarchical structures usually have superior mechanical properties. Herein, inspired by the macro–micro coupling deformation characteristics of biomaterials, novel hierarchical auxetic-hexagonal honeycombs (AuxHex) metamaterials with various substructures, including equilateral triangles and double arrowheads lattice cells, were constructed. A universal analysis model of the plastic collapse stress was first established, considering the deformation behavior of both the primary and secondary structures. This mechanism-based method gets rid of redundant numerical fitting parameters, and is applicable to different hierarchical lattice structures. Typical hierarchical AuxHex specimens were prepared using selected laser melting and stainless steel. In-plane compression tests and finite element simulation results demonstrated that, in contrast to the regular structures, hierarchical honeycombs exhibit enhancement in their load-bearing capacities and energy absorption ability. The specific modulus of T-AuxHex and A-AuxHex were increased by about 180% and 45%, the specific strength rose by approximately 50% and 15%, and the specific energy absorption was improved by about 160% and 50%. The effects of geometrical parameters were systematically discussed to reveal the mechanisms underlying the enhancement of the above mechanical characteristics. The proposed theoretical model provides a new method for designing the mechanical properties of hierarchical metamaterials by tailoring the type and distribution of secondary structures.

Analogue sandbox modeling of orogenic wedge front faulting: Roles of inherited fault zones and topographic loading

Earthquakes reported in the frontal belts of active orogenic wedges such as the 2013 Mw6.6 Lushan and 1999 Mw7.6 Chi-Chi earthquakes, highlight the importance of loading exerted by mountainous topography and inherited fault zones. However, their effects on formation and activation of these wedge front fault systems remain poorly understood. This study presents three sets of sandbox experiments in which topographic loading and geometry of inherited faults were first separately investigated, then explored jointly. Experiments show that smaller topographic loading favors gentle-dipping wedge front thrusts, while larger topographic loading promotes the development of steep wedge front faults. Introduced as zones of frictional weakness, all inherited faults promote deformation localization, though the steep ones are characterized by buttressing nearby rather than direct slip on themselves. When the two factors were tested integrally, four major deformation modes arose, including (1) direct reactivation; (2) fault truncation in the initial stage of compression; (3) stacking of small thrusts against the inherited fault and possible truncation in a later evolutionary stage; (4) behavior as a fossil structure. These modes show differences not only in first-order deformation styles, but also in the distribution of secondary structures, defining a basic framework and providing new guides for the interpretation of complex wedge front fault systems and their activities, in areas such as the Longmen Shan (eastern Tibet), the Tian Shan and the western margin of the Taiwan orogen.

A novel application of dissolved ozone flotation on sewage sludge thickening: Performance and mechanism investigation

Sludge thickening in sewage treatment plants is an essential step to reduce the sewage sludge volume and provide space for collaborative anaerobic digestion of sludge and other urban organic wastes. Dissolved ozone flotation (DOF) is a novel choice worthy of application in the field of sludge thickening. In order to investigate the effect of DOF thickening, the total solid content (TS %) was used to characterize the thickening performance under different O3 dosage. The optimal condition was determined to be polyacrylamide (PAM) dosage = 3 ‰ TS, air floatation time = 2 h and O3 dosage = 12 mg/g TS, under which the TS % of raw-sewage sludge (RS) increased from 0.33 ± 0.01 % to 8.03 ± 0.06 %. In this study, the relationship between the sludge thickening performance, physicochemical properties, and the changes of organic matter (content, structure and molecular weight) in extracellular polymers (EPS) was systematically clarified. The results indicated that the DOF couple with PAM could change the sludge surface properties, destroy the sludge floc structure, release intracellular organic matter, and increase moisture fluidity. The surface hydrophilicity/hydrophobicity, protein (PN) secondary structure and moisture distribution were mainly responsible for sludge thickening performance. Moreover, the change of TS % during the DOF thickening process was mainly caused by the variations of the organic matter content in EMPS layer. The identification of key influencing factors was conducive to the further regulation and upgrading of the novel application for enhanced sludge thickening in sewage treatment plants.

Changes in Biochemical Properties and Activity of Trypsin-like Protease (Litopenaeus vannamei) Treated by Atmospheric Cold Plasma (ACP).

The changes in the functional properties of trypsin from shrimps (Litopenaeus vannamei) after, Atmospheric Cold Plasma (ACP) treatments, have been evaluated in terms of enzyme inactivation, surface hydrophobicity, secondary structure, fluorescence intensity, and particle size distribution. Different exposure voltages of 10, 20, 30, 40, and 50 kV at various treatment times (1, 2, 3, and 4 min) have been employed, in a separate assay. The results showed that trypsin-like protease activity decreased (by about 50%), and the kinetic constants Km value increased, while the kcat value decreased. Surface hydrophobicity and fluorescence intensity revealed a significant increase compared to the control sample. A high degree of protein degradation has been noticed by SDS-PAGE analysis. In addition, circular dichroism indicated that random coil and α-helix contents declined while β-turn and β-sheet contents have raised. A sharp drop in the particle size was observed with increasing the treatment voltage from 0 to 40 kV for 4 min, and the corresponding peak reached the minimum of 531.2 nm. Summing up the results, it can be concluded that the ACP technique effectively affects the activity of trypsin-like protease, which in terms enhances the quality of dietary protein.

CICLOP: a robust and accurate computational framework for protein inner cavity detection

Abstract Motivation Internal cavities in proteins are of critical functional importance. They can serve as substrate/ligand-binding sites, pave path for movement of biomolecules and even mediate structural conformations occurring between domain interfaces during structural transitions. Yet, there is a paucity of computational tools that can accurately and reliably characterize the inner cavities of the proteins, a prerequisite for elucidating their functions. Results We have developed a novel method, CICLOP, that can accurately identify these regions at an atomistic resolution. The method is able to accurately detect residues lining the inner cavity, the diameter and volume occupied by the cavity, as well as physico-chemical properties of residues lining the cavity, such as their hydrophobicity and secondary structure distribution in detail. Additionally, our method also provides an option for computing conservation scores for the residues detected on the inside, allowing for a thorough functional characterization of the cavity. Availability and implementation CICLOP is available at http://ciclop.raylab.iiitd.edu.in/. A compiled Linux executable can be downloaded from https://ciclop.raylab.iiitd.edu.in/standalone/. Supplementary information Supplementary data are available at Bioinformatics online.

Effects of repeated freezing and thawing on myofibrillar protein and quality characteristics of marinated Enshi black pork

Repeated freeze–thaw is one of the main reasons for quality deterioration of frozen meat products. The study focused on the changes of endogenous fluorescence, secondary structure, microstructure, and water retention and distribution in marinated and unmarinated Enshi black pork after 10 freeze–thaw cycles. The results revealed that marinated treatment significantly reduced the thaw and centrifugal loss (P < 0.05), and increased endogenous fluorescence intensity of samples. During the entire freeze–thaw process, free water was undetectable in marinated group. After the first 4 cycles, α-helix percentage in marinated group was higher than that in control group. Scanning electron microscopy results suggested that there was no obvious increase in muscle fiber gap until 8 cycles in marinated group. Conclusively, moderate marination could slow down the deterioration of myofibrillar protein and pork quality, but it would be better to limit freeze–thaw cycles within 4 to maintain the quality of marinated Enshi black pork.

Low‐field NMR and FTIR determination relationship between water migration and protein conformation of the preparation of minced meat

SummaryThe low‐field nuclear magnetic resonance and Fourier transform infrared spectroscopy technique were carried out to evaluate the relationship between hydration characteristics and proteins structure in different stages pork of meat batters. The results showed that T21 increased throughout the process and the change of T22 and P21 was easily impacted by water, and the alternation of secondary structure was mostly impacted by salt; P21 was negatively correlated with the content of β‐sheet (r = −0.862), and positively correlated with the content of α‐helix (r = 0.933), β‐turn (r = 0.871) and random coil (r = 0.677), which meant there was some relationship between secondary structure and water distribution and migration. This research will provide theoretical support for the processing and production of meat products.