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The aim of the research is to examine the biophysical, spatial, functional, and structural components of the pre-Hispanic terracing systems located in the ancient city of Pisaq, considering the impacts of tourism, geological instability, and cultural loss on the ecological and economic value of the terracing system. The methodology includes site analysis, climatology, and an examination of local flora and fauna, supported by digital tools such as QGIS 3.34, Google Earth Pro 2024, and Sun-Path. The results were primarily supported by the use of software tools such as QGIS, AutoCAD 2023, SketchUp 2022, 3D Sun-Path, D5 Render 2024, and Photoshop 2021. The findings include a biophysical analysis related to ecological and economic zoning (EEZ), which determines variables for preservation and reforestation; a spatial analysis measuring the cultivation terraces, with areas ranging from 4.89 ha to 110.20 ha; a functional analysis examining geophysical aspects such as seismic resistance and microclimate effects due to the greenhouse effect; and a constructive analysis that characterizes terrace typologies from an architectural perspective. In conclusion, this analysis evaluates the terracing system of the archaeological park to ensure its preservation and effective management. It also highlights that Inca culture has left a legacy of sustainable architecture, which aligns with the current Sustainable Development Goals (SDGs) (6, 11, 13, 15). [ABSTRACT FROM AUTHOR]

Abstract Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes’ high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits.

Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes' high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits. [ABSTRACT FROM AUTHOR]

In this study, sub-watersheds of Manjira River basin in India is assessed for necessity of soil conservation studies by incorporating morphometric, biophysical and socioeconomic parameters using ArcGIS and Generalised Watershed Loading Function (GWLF) model. Morphometric parameters include watershed aspect, linear aspect, shape aspect and landscape aspect. The biophysical parameters considered are vegetation change, erosion and sediment loadings. The socioeconomic parameters considered are population density, literacy rate and agriculture worker density. The sub-basins were prioritized applying the Fuzzy Analytical Hierarchy Process (FAHP) into five priority classes, namely, "Very High", "High", "Medium", "Low" and "Very Low", covering approximately 36.4%, 15.5%, 24.4%, 11.39% and 11.28% of the surveyed area. An area of 2027.629 km2 was found to be in the very high risk priority class with respect to soil conservation management to be applied in the respective sub-basins. [ABSTRACT FROM AUTHOR]

Synthetic surfactants are used in several industries, including manufacturing, pharmaceutical and cosmetic’s, food and feed, agriculture, petroleum and environmental remediation for their ability to adsorb to fluid and solid-water interfaces. However, their widespread use and their synthetic preparation through environmentally unfavorable processes counterbalances the value of this class of reagents. This fact has stimulated new efforts to exploit natural sources of surfactants, such as new classes of bacterial systems or manipulation of existing biological systems, that may produce, through an environmentally friendly process, new biodegradable surfactants and emulsifiers of high commercial value. A downside of microbial production of biobased chemicals such as these types of chemicals, is that their fermentation often yields crude materials consisting of several bioproducts with complex physical and chemical properties. Extraction, identification, and efficient characterization of biosurfactants from a crude mixture of biomolecules requires carefully designed, and detailed analytical processes using state-of-the-art methods. The purpose of this review article is to present the current state-of-the-art and future outlook on the various multidisciplinary biophysical methods applied in the discovery, extraction identification, and in-depth characterization of microbially-produced surface‐active compounds.

Changes of biophysical and biochemical features in canopy cover over space and time can be used to elucidate watershed resilience to climate change or extreme weather. Geospatial technologies such as satellite remote sensing are helpful to identify such vegetation dynamics. This paper investigates the landfall impact of Hurricane Irma on canopy cover in the Santa Fe River Basin (Florida), which occurred in August 2017. Specifically, this study explores the effect of Hurricane Irma on vegetation dynamics via biophysical and biochemical features during the pre and post hurricane landfall. The geospatial analysis compares a suite of remote sensing spectral indices including enhanced vegetation index (EVI), leaf area index (LAI), fraction of photosynthetically active radiation (FPAR), evapotranspiration (ET), land surface temperature (LST), and global vegetation moisture index (GVMI). It is noticeable that paired spectral indices such as EVI-LST, GVMI-LST, LAI-LST, EVI-GVMI, EVI-LAI, LAI-FPAR, EVI-FPAR, and LAI-GVMI reflecting the dependent relationships between biophysical and biochemical features reveal varying level of logistic trends under Irma landfall impact. In addition, the evolution of these biophysical and biochemical features associated with the vegetation cover was analyzed in terms of the functional capacity over grassland, evergreen forested land, deciduous forested land, and agricultural land, to understand watershed response following Irma landfall. The functional capacity of the ecosystem reduced in terms of EVI and LAI over these four land-over patterns due to the landfall of Hurricane Irma. The interactions between agricultural land variation and flooding impact before and after the hurricane landfall further entail human impact on natural system in a food-water nexus.

Mutations in the SCN8A gene, encoding the voltage-gated sodium channel Na V 1.6, are associated with a range of neurodevelopmental syndromes. The p.(Gly1625Arg) (G1625R) mutation was identified in a patient diagnosed with developmental epileptic encephalopathy (DEE). While most of the characterized DEE-associated SCN8A mutations were shown to cause a gain-of-channel function, we show that the G1625R variant, positioned within the S4 segment of domain IV, results in complex effects. Voltage-clamp analyses of Na V 1.6G1625R demonstrated a mixture of gain- and loss-of-function properties, including reduced current amplitudes, increased time constant of fast voltage-dependent inactivation, a depolarizing shift in the voltage dependence of activation and inactivation, and increased channel availability with high-frequency repeated depolarization. Current-clamp analyses in transfected cultured neurons revealed that these biophysical properties caused a marked reduction in the number of action potentials when firing was driven by the transfected mutant Na V 1.6. Accordingly, computational modeling of mature cortical neurons demonstrated a mild decrease in neuronal firing when mimicking the patients' heterozygous SCN8A expression. Structural modeling of Na V 1.6G1625R suggested the formation of a cation-π interaction between R1625 and F1588 within domain IV. Double-mutant cycle analysis revealed that this interaction affects the voltage dependence of inactivation in Na V 1.6G1625R. Together, our studies demonstrate that the G1625R variant leads to a complex combination of gain and loss of function biophysical changes that result in an overall mild reduction in neuronal firing, related to the perturbed interaction network within the voltage sensor domain, necessitating personalized multi-tiered analysis for SCN8A mutations for optimal treatment selection. [Display omitted] • The SCN8A G1625R mutation was identified in a child with mild epilepsy and profound developmental delay. • Voltage-clamp analyses demonstrated a mixture of gain- and loss-of-function properties. • Current-clamp analyses in transfected cultured neurons showed reduced firing. • Computational modeling revealed an overall loss-of-function effect. • The biophysical changes may be associated with the formation of cation-π interaction between R1625 and F1588. [ABSTRACT FROM AUTHOR]

There is currently a large panel of technologies available to address molecular interactions in vitro. Each technology presents individual advantages and drawbacks, and it becomes challenging to choose which technology will be best suited for a molecular interaction of interest. Approaches can be broadly categorized as either microfluidic surface-bound methods (such as Surface Plasmon Resonance (SPR) or switchSENSE) or in-solution methods (such as Isothermal Titration Calorimetry (ITC) or MicroScale Thermophoresis (MST)). In-solution methods are advantageous in terms of sample preparation and ease of use as none of the binding partners are subjected to immobilization. On the other hand, surface-based techniques require only small amounts of immobilized interaction partner and provide off-rate characterization as unbound analytes can be removed from the surface to observe analyte dissociation. Here, a standard operating procedure (SOP) for the switchSENSE method is presented, which aims to guide new users through the process of a switchSENSE measurement, covering sample preparation, instrument and biochip handling as well as data acquisition and analysis. This guide will help researchers decide whether switchSENSE is the right method for their application as well as supporting novice users to get the most information out of a switchSENSE measurement. switchSENSE technology offers the unique advantage of a controlled DNA-based ligand surface within a microfluidic channel which allows the user to distribute specifically up to two different ligand molecules on the surface at a customized density and ratio. The technology offers multi-parameter characterization of binding kinetics, affinity, enzymatic activity, and changes in protein conformation. [ABSTRACT FROM AUTHOR]

It is important to note that folic acid is an important molecule in terms of human health. Folic acid that is one of the important molecules in human body plays an important role in the prevention of birth defects of the baby's brain (anencephaly) and spine (spina bifida). This molecule that is a form of vitamin B-9 can be easily dissolved in water media. Besides the molecule have important roles in nucleic acid production. Folic acid that is a complex type of vitamin B takes charge in the creating more red blood cells, preventing hearing loss, and preserving the brain health of infants. Because of the importance of folic acids and its derivatives, in this study, we analyzed the chemical reactivity of folic acid and its derivatives using DFT and Molecular Docking Programmes and investigated the power of the interactions with some well- known target proteins of the aforementioned molecules. Folic acid and its cadmium, copper and mercury complexes are performed in molecular docking studies for the activity against creatine kinase target protein in human brain. [ABSTRACT FROM AUTHOR]

Drug resistance to almost all antibiotics of Shigella flexneri , a major cause of shigellosis in developing countries, necessitates continuous discovery of novel therapeutics. This study reports a structure-function analysis of a potential drug target serine acetyltransferase (CysE), an enzyme of de novo cysteine biosynthesis pathway that is absent in humans. Analysis of CysE sequences of S. flexneri species and serotypes displayed only two variants that differed by a single amino acid substitution at position 241. Structural inspection of the available crystal structure disclosed this site to be distinct from the substrate/cofactor binding pockets or dimer/trimer interfaces. This study discovers that V241 variant of S. flexneri CysE has nearly null enzymatic activity. The observation is explained by molecular dynamic studies which reveal that the disorder generated by A241V substitution is the basis of dissociation of the quaternary assembly of S. flexneri CysE leading to loss of enzymatic activity and stability. The study provides the first evidence that position 241 of CysE, affects the catalytic efficiency of enzyme and suggests this locus as a ‘hot spot’ for the propagation of conformational changes. It may be postulated that transient quaternary structure of CysE maybe another mechanism for regulating the intracellular level of cysteine. [ABSTRACT FROM AUTHOR]

CERES-Maize model was used to determine nitrogen fertilizer requirements of early maturing maize varieties in the Sudan Savanna. Data were collected from 2013 to 2014 field experiments conducted in Bayero University Kano, (BUK), Kano, Nigeria. The experiments consisted of three nitrogen fertilizer levels (0, 60, and 120 kg N ha−1) and two early maize varieties (EVDT and 2009 TZEEW). Sensitivity analysis was performed to evaluate the responses of the two maizes to N fertilizers and for economic and strategic responses. The model predicted grain yield and harvest index reasonably well for the two varieties. Increasing N application from 0 to 30 kg N ha−1increased grain yield by 105%, when nitrogen (N) rate was increased to 60 kg N ha−1, grain yield increased by 226%. Yield increases of 364%, 451%, and 461% was observed when N rate increased from 0 to 90, 120, and 150 kg ha−1, respectively. [ABSTRACT FROM PUBLISHER]

DNA minor-groove-binding compounds have limited biological applications, in part due to problems with sequence specificity that cause off-target effects. A model to enhance specificity has been developed with the goal of preparing compounds that bind to two AT sites separated by G·C base pairs. Compounds of interest were probed using thermal melting, circular dichroism, mass spectrometry, biosensor-SPR, and molecular modeling methods. A new minor groove binder that can strongly and specifically recognize a single G·C base pair with flanking AT sequences has been prepared. This multi-site DNA recognition mode offers novel design principles to recognize entirely new DNA motifs. [ABSTRACT FROM AUTHOR]

Recent human clinical trials results demonstrated successful treatment for certain genetic forms of cystic fibrosis (CF). To extend treatment opportunities to those afflicted with other genetic forms of CF disease, structural and biophysical characterization of CF transmembrane conductance regulator (CFTR) is urgently needed. In this study, CFTR was modified with various tags, including a His purification tag, the SUMOstar (SUMO*) domain, an extracellular FLAG epitope, and an enhanced green fluorescent protein (EGFP), each alone or in various combinations. Expressed in HEK293 cells, recombinant CFTR proteins underwent complex glycosylation, compartmentalized with the plasma membrane, and exhibited regulated chloride-channel activity with only modest alterations in channel conductance and gating kinetics. Surface CFTR expression level was enhanced by the presence of SUMO* on the N-terminus. Quantitative mass-spectrometric analysis indicated approximately 10 % of the total recombinant CFTR (SUMO*-CFTR-EGFP) localized to the plasma membrane. Trial purification using dodecylmaltoside for membrane protein extraction reproducibly recovered 178 ± 56 μg SUMO*-CFTR-EGFP per billion cells at 80 % purity. Fluorescence size-exclusion chromatography indicated purified CFTR was monodisperse. These findings demonstrate a stable mammalian cell expression system capable of producing human CFTR of sufficient quality and quantity to augment future CF drug discovery efforts, including biophysical and structural studies. [ABSTRACT FROM AUTHOR]

Correlation of thermodynamic and secondary structural stability of proteins at various buffer pHs was investigated using differential scanning calorimetry (DSC), dynamic light scattering (DLS) and attenuated total reflection Fourier-transform infrared spectroscopy (ATR FT-IR). Recombinant human epithelial growth factor (rhEGF) was selected as a model protein at various pHs and in different buffers, including phosphate, histidine, citrate, HEPES and Tris. Particle size and zeta potential of rhEGF at each selected pH of buffer were observed by DLS. Four factors were used to characterize the biophysical stability of rhEGF in solution: temperature at maximum heat flux ( Tm), intermolecular β-sheet contents, zeta size and zeta potential. It was possible to predict the apparent isoelectric point (pI) of rhEGF as 4.43 by plotting pH against zeta potential. When the pH of the rhEGF solution increased or decreased from pI, the absolute zeta potential increased indicating a reduced possibility of protein aggregation, since Tm increased and β-sheet contents decreased. The contents of induced intermolecular β-sheet in Tris and HEPES buffers were the lowest. Thermodynamic stability of rhEGF markedly increased when pH is higher than 6.2 in histidine buffer where Tm of first transition was all above 70 °C. Moreover, rhEGF in Tris buffer was more thermodynamically stable than in HEPES with higher zeta potential. Tris buffer at pH 7.2 was concluded to be the most favorable. [ABSTRACT FROM AUTHOR]

The trans-activator of transcription (TAT) peptide is regarded as the "gold standard" for cell-penetrating peptides, capable of traversing a mammalian membrane passively into the cytosolic space. This characteristic has been exploited through conjugation of TAT for applications such as drug delivery. However, the process by which TAT achieves membrane penetration remains ambiguous and unresolved. Mechanistic details of TAT peptide action are revealed herein by using three complementary methods: quartz crystal microbalance with dissipation (QCMD), scanning electrochemical microscopy (SECM) and atomic force microscopy (AFM). When combined, these three scales of measurement define that the membrane uptake of the TAT peptide is by trans-membrane insertion using a "worm-hole" pore that leads to ion permeability across the membrane layer. AFM data provided nanometre-scale visualisation of TAT punctuation using a mammalian-mimetic membrane bilayer. The TAT peptide does not show the same specificity towards a bacterial mimetic membrane and QCM-D and SECM showed that the TAT peptide demonstrates a disruptive action towards these membranes. This investigation supports the energy-independent uptake of the cationic TAT peptide and provides empirical data that clarify the mechanism by which the TAT peptide achieves its membrane activity. The novel use of these three biophysical techniques provides valuable insight into the mechanism for TAT peptide translocation, which is essential for improvements in the cellular delivery of TAT-conjugated cargoes including therapeutic agents required to target specific intracellular locations. [ABSTRACT FROM AUTHOR]

Abstract: Interestingly, our previously published structure of the coil 1A fragment of the human intermediate filament protein vimentin turned out to be a monomeric α-helical coil instead of the expected dimeric coiled coil. However, the 39-amino-acid-long helix had an intrinsic curvature compatible with a coiled coil. We have now designed four mutants of vimentin coil 1A, modifying key a and d positions in the heptad repeat pattern, with the aim of investigating the molecular criteria that are needed to stabilize a dimeric coiled-coil structure. We have analysed the biophysical properties of the mutants by circular dichroism spectroscopy, analytical ultracentrifugation and X-ray crystallography. All four mutants exhibited an increased stability over the wild type as indicated by a rise in the melting temperature (T m). At a concentration of 0.1 mg/ml, the T m of the peptide with the single point mutation Y117L increased dramatically by 46 °C compared with the wild-type peptide. In general, the introduction of a single stabilizing point mutation at an a or a d position did induce the formation of a stable dimer as demonstrated by sedimentation equilibrium experiments. The dimeric oligomerisation state of the Y117L peptide was furthermore confirmed by X-ray crystallography, which yielded a structure with a genuine coiled-coil geometry. Most notably, when this mutation was introduced into full-length vimentin, filament assembly was completely arrested at the unit-length filament (ULF) level, both in vitro and in cDNA-transfected cultured cells. Therefore, the low propensity of the wild-type coil 1A to form a stable two-stranded coiled coil is most likely a prerequisite for the end-to-end annealing of ULFs into filaments. Accordingly, the coil 1A domains might “switch” from a dimeric α-helical coiled coil into a more open structure, thus mediating, within the ULFs, the conformational rearrangements of the tetrameric subunits that are needed for the intermediate filament elongation reaction. [Copyright &y& Elsevier]

A new method for measuring fruit-to-fruit variation in strawberries by both sensory and instrumental analyses was developed and applied. The method allowed quantification of fruit-to-fruit variation in sensory attributes and instrumental properties. Two commercial colour gradings (3/4 and 4/4 red) of strawberry commonly used at harvest were investigated. In the main experiment, one-half of a strawberry fruit was assessed for sensory characteristics by a trained panel while the other half was concurrently individually evaluated for soluble solids content (SSC), pH, titratable acidity (TA), firmness, and headspace volatile composition. The sensory evaluation was additionally performed on a bulk purée of fruit from the same harvest and the results were compared with the sensory evaluation on individual fruit. This study suggests that fruit-to-fruit variation is substantial in SSC, TA and fruit firmness and sensory characteristics such as ‘fruity odour’, ‘sweet flavour’ and ‘flavour aftertaste’, whereas other characteristics show similar variation among panellists for both individual fruit and bulk purée analyses. Further, individual fruit flavour characteristics were correlated with fruit biophysical properties. The results obtained are specific to this study and further investigations need to be undertaken to validate this method as a model for fruit-to-fruit variation in small fruit. [Copyright &y& Elsevier]

Abstract: Clinically used low molecular weight heparins (LMWH) are anticoagulants of choice and are phenomenally complex mixtures of millions of distinct natural and unnatural polymeric sequences. The FDA recommends that each LMWH be considered as an independent drug with its own activity profile, placing significant importance on the biophysical characterization of each intact LMWH. We report a robust protocol for fingerprinting these pharmaceutical agents. Capillary electrophoresis of three LMWHs, enoxaparin, tinzaparin, and a Sigma preparation, under reverse polarity conditions in the presence of selected linear alkyl polyamines gives an electrophoretic pattern that is characteristic of the nature of the starting material. The buffers that best provided optimal resolution without compromising sensitivity and speed of analysis were 50mM sodium phosphate, pH 2.3, and 100mM ammonium formate, pH 3.5. Resolution was strongly dependent on the structure of polyamine with pentaethylenehexamine being most effective for enoxaparin and Sigma LMWH. In contrast, tinzaparin could be best resolved with tetraethylenepentamine. Cyclic polyamines were ineffective. Resolution was also dependent on the concentration of resolving agents and displayed a narrow window that provides optimal resolution. These features suggest a strong structural origin of the fingerprint pattern. Overall, the simple protocol will find special use in assessing LMWH quality and batch-to-batch variability. [Copyright &y& Elsevier]

Diverse Gram-negative bacteria use type III secretion systems (T3SS) to translocate effector proteins into the cytoplasm of eukaryotic cells. The type III secretion apparatus (T3SA) consists of a basal body spanning both bacterial membranes and an external needle. A sensor protein lies at the needle tip to detect environmental signals that trigger type III secretion. The Shigella flexneri T3SA needle tip protein, invasion plasmid antigen D (IpaD), possesses two independently folding domains in vitro. In this study, the solution behavior and thermal unfolding properties of IpaD's functional homologs SipD ( Salmonella spp.), BipD ( Burkholderia pseudomallei), LcrV ( Yersinia spp.), and PcrV ( Pseudomonas aeruginosa) were examined to identify common features within this protein family. CD and FTIR data indicate that all members within this group are α-helical with properties consistent with an intramolecular coiled-coil. SipD showed the most complex unfolding profile consisting of two thermal transitions, suggesting the presence of two independently folding domains. No evidence of multiple folding domains was seen, however, for BipD, LcrV, or PcrV. Thermal studies, including DSC, revealed significant destabilization of LcrV, PcrV, and BipD after N-terminal deletions. This contrasted with SipD and IpaD, which behaved like two-domain proteins. The results suggest that needle tip proteins share significant core structural similarity and thermal stability that may be the basis for their common function. Moreover, IpaD and SipD possess properties that distinguish them from the other tip proteins. [ABSTRACT FROM AUTHOR]

Purpose: To determine biophysical parameters from the complication probability data during and after radiotherapy of Hodgkin’s lymphoma (HL), based on the number of gastrointestinal side effects that were found in the multicenter HD8 trial of the German Hodgkin Lymphoma Study Group. Methods and Materials: Between 1993 and 1998, 1204 patients with newly diagnosed, histology-proven HL in clinical Stages I/IIA/IIB with defined risk factors and stage IIIA without risk factors were enrolled into the multicenter HD8 study. Patients were randomized to receive two cycles of COPP (cyclophosphamide, vincristine, procarbazine, prednisone) alternating with two cycles of ABVD (doxorubicin, bleomycin, vinblastine, dacarbazine) followed by radiotherapy (RT) of 30 Gy extended field plus 10 Gy to bulky disease (Arm A) or 30 Gy involved field plus 10 Gy to bulky disease (Arm B). For 910 patients, the rates of acute gastrointestinal side effects during and after RT could be determined. Comparison showed differences between Arms A and B (Grade 1–2: 16.6 vs. 3.9; Grade 3–4: 0.9 vs. 0.2; p < 0.001). From the dose–volume histograms for a “standard patient” (volume intestine 2300 cm3), we determined the normal tissue complication probability (NTCP) (V, D, m, n, TD50 ), the biophysical parameter TD50 , and n (volume dependent) in such a manner that the observed NTCP in Arm A in cases of supradiaphragmatic involvement only and in cases of infradiaphragmatic involvement correlated with the calculated values. Results: Of 1,204 patients randomized, 1,064 patients were informative for the comparison of study arms. The median observation time was 54 months. The overall survival for all eligible patients was 91%, and freedom from treatment failure was 83%. Survival rates at 5 years after start of RT revealed no differences in terms of freedom from treatment failure (85.8% in Arm A, 84.2% in Arm B) and overall survival (90.8% and 92.4%). There were also no differences between the two arms in terms of complete remission, progressive disease, relapse, death, and secondary neoplasias. In contrast, acute side effects, including leukopenia, thrombocytopenia, nausea, gastrointestinal toxicity, and pharyngeal toxicity, were more frequent in the extended field arm. Concerning gastrointestinal toxicity, the different radiation treatment volumes resulted in different NTCPs. On the basis of these findings, values of n = 0.09 and TD50 = 32 Gy were derived. However, this biophysical model is sensitive to variations of the parameters. A deviation of 1% of TD50 results in a deviation of 10% of the NTCP. Conclusion Radiotherapy volume reduction from extended field to involved field after two cycles of COPP/ABVD chemotherapy gives similar results and less toxicity in patients with early-stage, unfavorable HL. Biophysical parameters could be determined from the complication probability data after RT of HL. Because of the exponential dependence, this biophysical model is unstable. It represents a “start model” until further data can be incorporated. [Copyright &y& Elsevier]

We report the structural and biophysical consequences of cysteine substitutions in the DNA-binding replication terminator protein (RTP) of Bacillus subtilis, that resulted in an optimised RTP mutant suitable for structural studies. The cysteine residue 110 was replaced with alanine, valine or serine. Protein secondary structure and stability (using circular dichroism spectropolarimetry), self-association (using analytical ultracentrifugation), and DNA-binding measurements revealed RTP.C110S to be the most similar mutant to wild-type RTP. The C110A and C110V.RTP mutants were less soluble, less stable and showed lower DNA-binding affinity. The structure of RTP.C110S, solved to 2.5 A˚ resolution using crystallographic methods, showed no major structural perturbation due to the mutation. Heteronuclear NMR spectroscopic studies revealed subtle differences in the electronic environment about the site of mutation. The study demonstrates the suitability of serine as a substitute for cysteine in RTP and the high sensitivity of protein behaviour to single amino acid substitutions. [Copyright &y& Elsevier]

Cloxyquin is a potential therapeutic compound possessing various bioactivities, especially antibacterial, antifungal, cardioprotective, and pain relief activities. Herein, the interaction mechanism between cloxyquin and bovine serum albumin (BSA) has been elucidated in order to fulfill its pharmacokinetic and pharmacodynamic gaps essential for further development as a therapeutic drug. Multi-spectroscopic and biophysical model analysis suggested that cloxyquin interacts with BSA via a static process by ground-state complex formation. Its binding behavior emerged as a biphasic fashion with a moderate binding constant at the level of 104 M−1. Thermodynamic analysis and molecular docking simulation concurrently revealed that hydrophobic interaction is a major driving force for BSA–cloxyquin complexation. Binding of cloxyquin tends to slightly enlarge the monomeric size of BSA without a significant increase of aggregate fraction. Cloxyquin preferentially binds into the fatty acid binding site 5 (FA5) of the BSA via hydrophobic interaction amongst its quinoline scaffold and Phe550, Leu531, and Leu574 residues of BSA. The quinoline ring and hydroxyl moiety of cloxyquin also form the π–π interaction and the hydrogen bond with Phe506. Our data indicate a potential function of serum albumin as a carrier of cloxyquin in blood circulation. [ABSTRACT FROM AUTHOR]

Summary α-Synuclein (αSN) aggregation is central to the etiology of Parkinson's disease (PD). Large-scale screening of compounds to identify aggregation inhibitors is challenged by stochastic αSN aggregation and difficulties in detecting early-stage oligomers (αSOs). We developed a high-throughput screening assay combining SDS-stimulated αSN aggregation with FRET to reproducibly detect initial stages in αSN aggregation. We screened 746,000 compounds, leading to 58 hits that markedly inhibit αSN aggregation and reduce αSOs' membrane permeabilization activity. The most effective aggregation inhibitors were derivatives of (4-hydroxynaphthalen-1-yl)sulfonamide. They interacted strongly with the N-terminal part of monomeric αSN and reduced αSO-membrane interactions, possibly by affecting electrostatic interactions. Several compounds reduced αSO toxicity toward neuronal cell lines. The inhibitors introduced chemical modifications of αSN that were, however, not a prerequisite for inhibitory activity. We also identified several phenyl-benzoxazol compounds that promoted αSN aggregation (proaggregators). These compounds may be useful tools to modulate αSN aggregation in cellula. Graphical Abstract Highlights • Developed an FRET-based high-throughput screen for inhibitors of αSN aggregation • The six best hits share a (4-hydroxynaphthalen-1-yl)sulfonamide core structure • These hits interact with αSN's N-region and reduce oligomer-membrane interactions • The two best aggregation promoters (proaggregators) share a phenyl-benzoxazol core Kurnik et al. developed an FRET-based high-throughput screen for inhibitors of α-synuclein aggregation, critical in development of Parkinson's disease. Out of 746,000 compounds, the 6 best hits are derivatives of (4-hydroxynaphthalen-1-yl)sulfonamide, interact with α-synuclein's N-region and reduce oligomer-membrane interactions. We also identified compounds promoting aggregation; the 2 best share a phenyl-benzoxazol core. [ABSTRACT FROM AUTHOR]

N-terminal acetylation is a co- and post-translational modification catalyzed by the conserved N-terminal acetyltransferase (NAT) family of enzymes. A majority of the human proteome is modified by the human NATs (NatA-F and H), which are minimally composed of a catalytic subunit and as many as two auxiliary subunits. Together, NATs specifically regulate many cellular functions by influencing protein activities such as their degradation, membrane targeting, and protein-protein interactions. This chapter will describe methods developed for their preparation, and their biochemical and structural characterization. This will include methodologies for expression and purification of recombinant NAT protein, kinetic assays, biochemical and biophysical assays, and strategies for structural studies., (© 2019 Elsevier Inc. All rights reserved.)

In small molecule drug discovery, researchers must find specific binders that interact with a target protein and inhibit its function in connection with human diseases. It is of critical importance to know the binding mode of compounds interacting with a target protein to assure hit validation and optimization. Biophysical analysis is a powerful quantitative approach to evaluate the binding modes of such candidates. Since the level of sensitivity of biophysical analysis is suitable to quantitatively detect the binding of fragment compounds, and because of the remarkable success of compound libraries of small molecules, the development and adaptation of biophysical analysis for these applications is in great demand. Herein, we describe the technical developments of biophysical methods, especially thermodynamic and kinetic analysis, for the purpose of screenings which employ small molecules. In addition, we discuss the interaction mechanisms of small molecules to find hit compounds based on these biophysical analyses.