Conformational Distribution Research Articles

Modeling Alternative Conformational States of Pseudo-Symmetric Solute Carrier Transporters using Methods from Machine Learning.

The Solute Carrier (SLC) superfamily of integral membrane proteins function to transport a wide array of solutes across the plasma and organelle membranes. SLC proteins also function as important drug transporters and as viral receptors. Despite being classified as a single superfamily, SLC proteins do not share a single common fold classification; however, most belong to multi-pass transmembrane helical protein fold families. SLC proteins populate different conformational states during the solute transport process, including outward open, intermediate (occluded), and inward open conformational states. For some SLC fold families this structural "flipping" corresponds to swapping between conformations of their N-terminal and C-terminal symmetry-related sub-structures. Conventional AlphaFold2 or Evolutionary Scale Modeling methods typically generate models for only one of these multiple conformational states of SLC proteins. Here we describe a fast and simple approach for modeling multiple conformational states of SLC proteins using a combined ESM - AF2 process. The resulting multi-state models are validated by comparison with sequence-based evolutionary co-variance data (ECs) that encode information about contacts present in the various conformational states adopted by the protein. We also explored the impact of mutations on conformational distributions of SLC proteins modeled by AlphaFold2 using both conventional and enhanced sampling methods. This approach for modeling conformational landscapes of pseudo-symmetric SLC proteins is demonstrated for several integral membrane protein transporters, including SLC35F2 the receptor of a feline leukemia virus envelope protein required for viral entry into eukaryotic cells.

Different or the same? exploring the physicochemical properties and molecular mobility of celecoxib amorphous forms

The influence of different preparation methods on the physicochemical properties of amorphous solid forms have gained considerable attention, especially with recent publications on pharmaceutical polyamorphism. In the present study, we have investigated the possible occurrence of polyamorphism in the drug celecoxib (CEL) by investigating the thermal behavior, morphology, structure, molecular mobility and physical stability of amorphous CEL obtained by quench-cooling (QC), ball milling (BM) and spray drying (SD). Similar glass transition temperatures but different recrystallization behaviors were observed for CEL-QC, CEL-BM and CEL-SD using modulated differential scanning calorimetry analysis. A correlation between the different recrystallization behaviors of the three CEL amorphous forms and the respective distinct powder morphologies, was also found. Molecular dynamics simulations however, reveal that CEL presents similar molecular conformational distributions when subjected to QC and SD. Moreover, the obtained molecular conformational distributions of CEL are different from the ones found in its crystal structure and also from the ones found in the lowest-energy structure obtained by quantum mechanical calculations. The type and strength of CEL hydrogen bond interactions found in CEL-QC and CEL-SD systems are almost identical, though different from the ones presented in the crystal structure. Pair distribution function analyses and isothermal microcalorimetry show similar local structures and structural relaxation times, respectively, for CEL-QC, CEL-BM and CEL-SD. The present work shows that not only similar physicochemical properties (glass transition temperature, and structural relaxation time), but also similar molecular conformational distributions were observed for all prepared CEL amorphous systems. Hence, despite their different recrystallization behaviors, the three amorphous forms of CEL did not show any signs of polyamorphism.

Computer-aided drug design supporting sunscreen research: a showcase study using previously synthesized hybrid UV filter-antioxidant compounds.

Although quantum mechanical calculations have proven effective in accurately predicting UV absorption and assessing the antioxidant potential of compounds, the utilization of computer-aided drug design (CADD) to support sustainable synthesis research of new sunscreen active ingredients remains an area with limited exploration. Furthermore, there are ongoing concerns about the safety and effectiveness of existing sunscreens. Therefore, it remains crucial to investigate photoprotection mechanisms and develop enhanced strategies for mitigating the harmful effects of UVR exposure, improving both the safety and efficacy of sunscreen products. A previous study conducted synthesis research on eight novel hybrid compounds (I-VIII) for use in sunscreen products by molecular hybridization of trans-resveratrol (RESV), avobenzone (AVO), and octinoxate (OMC). Herein, time-dependent density functional theory (TD-DFT) calculations performed in the gas phase on the isolated hybrid compounds (I-VIII) proved to reproduce the experimental UV absorption. Resveratrol-avobenzone structure-based hybrids (I-IV) present absorption maxima in the UVB range with slight differences between them, while resveratrol-OMC structure-based hybrids (V-VIII) showed main absorption in the UVA range. Among RESV-OMC hybrids, compounds V and VI exhibited higher UV absorption intensity, and compound VIII stood out for its broad-spectrum coverage in our simulations. Furthermore, both in silico and in vitro analyses revealed that compounds VII and VIII exhibited the highest antioxidant activity, with compound I emerging as the most reactive antioxidant within RESV-AVO hybrids. The study suggests a preference for the hydrogen atom transfer (HAT) mechanism over single-electron transfer followed by proton transfer (SET-PT) in the gas phase. With a strong focus on sustainability, this approach reduces costs and minimizes effluent production in synthesis research, promoting the eco-friendly development of new sunscreen active ingredients. The SPARTAN'20 program was utilized for the geometry optimization and energy calculations of all compounds. Conformer distribution analysis was performed using the Merck molecular force field 94 (MMFF94), and geometry optimization was carried out using the parametric method 6 (PM6) followed by density functional theory (DFT/B3LYP/6-31G(d)). The antioxidant behavior of the hybrid compounds (I-VIII) was determined using the highest occupied molecular orbital (εHOMO) and the lowest unoccupied molecular orbital (εLUMO) energies, as well as the bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) values, all calculated at the same level of structural optimization. TD-DFT study is carried out to calculate the excitation energy using the B3LYP functional with the 6-31G(d) basis set. The calculated transitions were convoluted with a Gaussian profile using the Gabedit program.

In Silico Determination of The Antifungal Effect of Plant Active Molecules Against Botrytis Cinerea by Molecular Docking

Botrytis cinerea, which has developed many strategies to infect plants, can survive in harsh environmental conditions, and has a wide host range, has become an important problem both economically and ecologically by causing tons of crop losses for many years. The residues in soil and crops caused by chemical pesticides used to get rid of agricultural pests pose serious threats to human and environmental health, such as hormonal abnormalities and acute respiratory poisoning, especially in children. The most critical step to avoid these hazards will be to replace chemical pesticides with plant-active molecules. At the same time, these studies primarily in silico will provide a return in terms of both time and cost. Inhibition of pectin methyl esterase, an important virulence factor of B. cinerea, will ensure the organism is controlled. In order to determine candidate biofungicide effector molecules, QSAR parameter values of 409 plant active molecules were calculated. Firstly, conformer distribution and geometry optimizations were performed with Spartan 14’ software. Docking studies of the optimized molecules were carried out through Autodock Vina software, while visualization studies to make sense of the interactions between the target receptor structure and effector molecules were used by BIOVIA Discovery Studio software. As a result of all the analyses, the molecules that are alternatives to chemical pesticides as biofungicides were determined to be the following molecules: Podolactone B, Repin, Sandaracopimaradienediol, 6-Hydrogenistein, Artemisinin, Lycoricidine, 6-Methoxygossypol, Viscidulin, Ciprofloxacin, and 7,4’-Dihydroxyflavan.

Broadening access to small-molecule parameterization with the force field toolkit.

Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable.

Intrinsic Conformational Dynamics of Glycine and Alanine in Polarizable Molecular Dynamics Force Fields: Comparison to Spectroscopic Data.

Molecular dynamics (MD) is a great tool for elucidating conformational dynamics of proteins and peptides in water at the atomistic level that often surpasses the level of detail available experimentally. Structure predictions, however, are limited by the accuracy of the underlying MD force field. This limitation is particularly stark in the case of intrinsically disordered peptides and proteins, which are characterized by solvent-accessible and disordered peptide regions and domains. Recent studies show that most additive MD force fields, including CHARMM36m, do not reproduce the intrinsic conformational distributions of guest amino acid residues x in cationic GxG peptides in water in line with experimental data. Positing that a lack of polarizability in additive MD force fields may be the culprit for the reported discrepancies, we here examine the conformational dynamics of guest glycine and alanine residues in cationic GxG peptides in water using two polarizable MD force fields, CHARMM Drude and AMOEBA. Our results indicate that while AMOEBA captures the experimental data better than CHARMM Drude, neither of the two polarizable force fields offers an improvement of the Ramachandran distributions of glycine and alanine residues in cationic GGG and GAG peptides, respectively, over CHARMM36m.

An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.

Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against Covid-19. During ribosomal translation, a fraction of elongating ribosomes slips by one base in the 5' direction and enters a new reading frame for viral protein synthesis. Any interference with this process profoundly affects viral replication and propagation. For Covid-19, two RNA sites associated with ribosomal frameshifting for SARS-CoV-2 are positioned on the 5' and 3' of the frameshifting residues. Although much attention has been on the 3' frameshift element (FSE), the 5' stem-loop (attenuator hairpin, AH) can play a role. The formation of AH has been suggested to occur as refolding of the 3' RNA structure is triggered by ribosomal unwinding. However, the attenuation activity and the relationship between the two regions are unknown. To gain more insight into these two related viral RNAs and to further enrich our understanding of ribosomal frameshifting for SARS-CoV-2, we explore the RNA folding of both 5' and 3' regions associated with frameshifting. Using our graph-theory-based modeling tools to represent RNA secondary structures, "RAG" (RNA- As-Graphs), and conformational landscapes to analyze length-dependent conformational distributions, we show that AH coexists with the 3-stem pseudoknot of the 3' FSE (graph 3_6 in our dual graph notation) and alternative pseudoknot (graph 3_3) but less likely with other 3' FSE alternative folds (such as 3-way junction 3_5). This is because an alternative length-dependent Stem 1 (AS1) can disrupt the FSE pseudoknots and trigger other folds. In addition, we design four mutants for long lengths that stabilize or disrupt AH, AS1 or FSE pseudoknot to illustrate the deduced AH/AS1 roles and favor the 3_5, 3_6 or stem-loop. These mutants further show how a strengthened pseudoknot can result from a weakened AS1, while a dominant stem-loop occurs with a strengthened AS1. These structural and mutational insights into both ends of the FSE in SARS-CoV-2 advance our understanding of the SARS-CoV-2 frameshifting mechanism by suggesting a sequence of length-dependent folds, which in turn define potential therapeutic intervention techniques involving both elements. Our work also highlights the complexity of viral landscapes with length-dependent folds, and challenges in analyzing these multiple conformations.

Dose conformity and falloff in single-lesion intracranial SRS with DCA and VMAT methods.

Intracranial stereotactic radiosurgery (SRS) aims at achieving highly conformal dose distribution and, at the same time, attaining rapid dose falloff outside the treatment target. SRS is performed using different techniques including dynamic conformal arcs (DCA) and volumetric modulated arc therapy (VMAT). In this study, we compare dose conformity and falloff in DCA and VMAT plans for SRS with a single target. To compare dose conformity in SRS plans, we employ a novel conformity index , RTOG conformity index ( ), and Riet-Paddick conformity index ( ). In addition, we use indices , , and to evaluate dose falloff. For each of the considered 118 cases of SRS, two plans were created using DCA and VMAT. A two-tailed Student's t-test was used to evaluate the difference between the employed indices for the DCA and VMAT plans. The studied VMAT plans were characterized by higher dose conformity than the DCA plans. The differences between the conformity indices for the DCA plans and VMAT plans were statistically significant. The DCA plans had a smaller number of monitor units (MUs) and smaller indices R50%, V10 Gy, and V12 Gy than the VMAT plans. However, the differences between R50%, V10 Gy, and V12 Gy for the DCA and VMAT plans were not statistically significant. Although the studied VMAT plans had higher dose conformity, they also had larger MUs than the DCA plans. In terms of dose falloff characterized by parameters R50%, V10 Gy, and V12 Gy, DCA serves as a reasonable alternative to VMAT in the case of a single brain metastasis.

Resolution in cryogenic solid state NMR: Challenges and solutions.

NMR at cryogenic temperatures has the potential to provide rich site-specific details regarding biopolymer structure, function, and mechanistic intermediates. Broad spectral lines compared with room temperature NMR can sometimes present practical challenges. A number of hypotheses regarding the origins of line broadening are explored. One frequently considered explanation is the presence of inhomogeneous conformational distributions. Possibly these arise when the facile characteristic motions that occur near room temperature become dramatically slower or "frozen out" at temperatures below the solvent phase change. Recent studies of low temperature spectra harness the distributions in properties in these low temperature spectra to uncover information regarding the conformational ensembles that drive biological function.

Elucidating the Molecular Basis of 14-3-3 Interaction with α-Synuclein: Insights from Molecular Dynamics Simulations and the Design of a Novel Protein-Protein Interaction Inhibitor.

Parkinson's disease is a widespread age-related neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain along with the appearance of protein aggregates, termed as "Lewy bodies" in the surviving neuronal cells. The components of Lewy bodies include proteins such as α-synuclein, 14-3-3, Parkin, and LRRK2, along with other cellular organelles, which, in their native state, perform a plethora of vital biological functions within the human biome. Formation of these aggregates renders these components inactive, thereby interfering with homeostasis. In this regard, the current study attempts to investigate the complexation behavior of all human-based 14-3-3 isoforms with α-synuclein via a combination of classical and enhanced sampling techniques and thereby determine the causality of these protein-protein interactions. The study indicated that upon complexation, the aggregation propensity of both 14-3-3 and α-synuclein increases, and this increment is propelled by the interfacial residues on either protein. Furthermore, mutagenesis studies revealed that Lys214 of 14-3-3 (henceforth termed K214A) is crucial for the formation of this binary complex. Principal component analysis combined with clustering studies unveiled the stability of these complexes in terms of their conformational distribution across the entire MD trajectory. For K214A, these clustered states were sparsely located, thereby making the transitions between them slightly difficult. Dynamic cross-correlation maps (DCCM) revealed the role of residues in the range 80-130 of 14-3-3 having a potential allosteric role in driving this complexation process. Finally, a novel peptide-based supramolecular inhibitor was designed, which exhibited higher proficiency in limiting the 14-3-3/α-synuclein interaction compared to the previous inhibitor model. It was also revealed that the presence of this inhibitor induces structural rigidity in α-synuclein, making changes in its conformations extremely difficult, as observed through Umbrella Sampling studies. Based on available information, the current study provides an insight into the molecular-level understanding of protein-protein interactions underlying Parkinson's disease and adds on to the methods of devising novel therapeutic approaches to treat the same.

HyperArcTM volumetric modulated arc therapy for hypopharyngeal cancer with solitary recurrence in the cervical vertebra: A case report and literature review.

It is difficult to reirradiate head and neck cancers because of the toxicity from previous radiation dose delivery. Conventional volumetric modulated arc therapy (VMAT) and intensity-modulated radiation therapy often have poor target coverage. The new HyperArcTM VMAT (HA-VMAT) planning approach reportedly has better target coverage, higher conformity, and can spare normal organs compared to conventional VMAT; however, research on recurrent head and neck cancers is limited. Here, we report the clinical outcomes of HA-VMAT for previously irradiated hypopharyngeal cancer with solitary recurrence in the first cervical vertebra (C1). A 52-year-old Asian male was diagnosed with a hypopharyngeal cancer. The patient received concurrent chemoradiotherapy with a radiation dose of 70 Gy in 33 fractions and achieved complete clinical response. Two years later, solitary recurrence was observed in the C1 vertebra. Solitary recurrence in the C1 vertebra. Owing to concerns regarding the toxicity to adjacent organs, we decided to use HA-VMAT to achieve better tumor coverage and critical organ sparing. Tumor regression was observed on the imaging. At 9 months follow-up, the patient was disease-free and had no late toxicities. This is the first report regarding the clinical outcomes of HA-VMAT for previously irradiated hypopharyngeal cancer with solitary recurrence over the C1 vertebra. HA-VMAT achieves highly conformal dose distribution and excellent sparing of critical organs. There was a favorable initial clinical response with no toxicity. Long-term follow-up is essential in such cases.

Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction

Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes being major antimicrobial drug targets. Here we compare two E. coli strains, a lab E. coli K-12 and human gut isolate E. coli ED1a, for which tetracycline exhibits bacteriostatic and bactericidal action, respectively. Using our approach for close-to-native E. coli sample preparation, we assess the two strains by cryo-ET and visualize their ribosomes at high resolution in situ. Upon tetracycline treatment, these exhibit virtually identical drug binding sites, yet the conformation distribution of ribosomal complexes differs. While K-12 retains ribosomes in a translation-competent state, tRNAs are lost in the vast majority of ED1a ribosomes. These structural findings together with the proteome-wide abundance and thermal stability assessments indicate that antibiotic responses are complex in cells and can differ between different strains of a single species, thus arguing that all relevant bacterial strains should be analyzed in situ when addressing antibiotic mode of action.

Attention 3D U-NET for dose distribution prediction of high-dose-rate brachytherapy of cervical cancer: Direction modulated brachytherapy tandem applicator.

Direction Modulated Brachytherapy (DMBT) enables conformal dose distributions. However, clinicians may face challenges in creating viable treatment plans within a fast-paced clinical setting, especially for a novel technology like DMBT, where cumulative clinical experience is limited. Deep learning-based dose prediction methods have emerged as effective tools for enhancing efficiency. To develop a voxel-wise dose prediction model using an attention-gating mechanism and a 3D UNET for cervical cancer high-dose-rate (HDR) brachytherapy treatment planning with DMBT six-groove tandems with ovoids or ring applicators. A multi-institutional cohort of 122 retrospective clinical HDR brachytherapy plans treated to a prescription dose in the range of 4.8-7.0Gy/fraction was used. A DMBT tandem model was constructed and incorporated onto a research version of BrachyVision Treatment Planning System (BV-TPS) as a 3D solid model applicator and retrospectively re-planned all cases by seasoned experts. Those plans were randomly divided into 64:16:20 as training, validating, and testing cohorts, respectively. Data augmentation was applied to the training and validation sets to increase the size by a factor of 4. An attention-gated 3D UNET architecture model was developed to predict full 3D dose distributions based on high-risk clinical target volume (CTVHR) and organs at risk (OARs) contour information. The model was trained using the mean absolute error loss function, Adam optimization algorithm, a learning rate of 0.001, 250 epochs, and a batch size of eight. In addition, a baseline UNET model was trained similarly for comparison. The model performance was evaluated on the testing dataset by analyzing the outcomes in terms of mean dose values and derived dose-volume-histogram indices from 3D dose distributions and comparing the generated dose distributions against the ground-truth dose distributions using dose statistics and clinically meaningful dosimetric indices. The proposed attention-gated 3D UNET model showed competitive accuracy in predicting 3D dose distributions that closely resemble the ground-truth dose distributions. The average values of the mean absolute errors were 1.82±29.09Gy (vs. 6.41±20.16Gy for a baseline UNET) in CTVHR, 0.89±1.25Gy (vs. 0.94±3.96Gy for a baseline UNET) in the bladder, 0.33±0.67Gy (vs. 0.53±1.66Gy for a baseline UNET) in the rectum, and 0.55±1.57Gy (vs. 0.76±2.89Gy for a baseline UNET) in the sigmoid. The results showed that the mean absolute error (MAE) for the bladder, rectum, and sigmoid were 0.22±1.22Gy (3.62%) (p=0.015), 0.21±1.06Gy (2.20%) (p=0.172), and -0.03±0.54Gy (1.13%) (p=0.774), respectively. The MAE for D90, V100%, and V150% of the CTVHR were 0.46±2.44Gy (8.14%) (p=0.018), 0.57±11.25% (5.23%) (p=0.283), and -0.43±19.36% (4.62%) (p=0.190), respectively. The proposed model needs less than 5 s to predict a full 3D dose distribution of 64×64×64 voxels for any new patient plan, thus making it sufficient for near real-time applications and aiding with decision-making in the clinic. Attention gated 3D-UNET model demonstrated a capability in predicting voxel-wise dose prediction, in comparison to 3D UNET, for DMBT intracavitary brachytherapy planning. The proposed model could be used to obtain dose distributions for near real-time decision-making before DMBT planning and quality assurance. This will guide future automated planning, making the workflow more efficient and clinically viable.

Technical note: Dosimetry and FLASH potential of UHDR proton PBS for small lung tumors: Bragg-peak-based delivery versus transmission beam and IMPT.

High-energy transmission beams (TBs) are currently the main delivery method for proton pencil beam scanning ultrahigh dose-rate (UHDR) FLASH radiotherapy. TBs place the Bragg-peaks behind the target, outside the patient, making delivery practical and achievement of high dose-rates more likely. However, they lead to higher integral dose compared to conventional intensity-modulated proton therapy (IMPT), in which Bragg-peaks are placed within the tumor. It is hypothesized that, when energy changes are not required and high beam currents are possible, Bragg-peak-based beams can not only achieve more conformal dose distributions than TBs, but also have more FLASH-potential. This works aims to verify this hypothesis by taking three different Bragg-peak-based delivery techniques and comparing them with TB and IMPT-plans in terms of dosimetry and FLASH-potential for single-fraction lung stereotactic body radiotherapy (SBRT). For a peripherally located lung target of various sizes, five different proton plans were made using "matRad" and inhouse-developed algorithms for spot/energy-layer/beam reduction and minimum monitor unit maximization: (1) IMPT-plan, reference for dosimetry, (2) TB-plan, reference for FLASH-amount, (3) pristine Bragg-peak plan (non-depth-modulated Bragg-peaks), (4) Bragg-peak plan using generic ridge filter, and (5) Bragg-peak plan using 3D range-modulated ridge filter. Bragg-peak-based plans are able to achieve sufficient plan quality and high dose-rates. IMPT-plans resulted in lowest OAR-dose and integral dose (also after a FLASH sparing-effect of 30%) compared to both TB-plans and Bragg-peak-based plans. Bragg-peak-based plans vary only slightly between themselves and generally achieve lower integral dose than TB-plans. However, TB-plans nearly always resulted in lower mean lung dose than Bragg-peak-based plans and due to a higher amount of FLASH-dose for TB-plans, this difference increased after including a FLASH sparing-effect. This work indicates that there is no benefit in using Bragg-peak-based beams instead of TBs for peripherally located, UHDR stereotactic lung radiotherapy, if lung dose is the priority.

Probability Density Reweighting of High-Temperature Molecular Dynamics.

Molecular dynamics (MD) simulation is a popular method for elucidating the structures and functions of biomolecules. However, exploring the conformational space, especially for large systems with slow transitions, often requires enhanced sampling methods. Although conducting MD at high temperatures provides a straightforward approach, resulting conformational ensembles diverge significantly from those at low temperatures. To address this discrepancy, we propose a novel probability density-based reweighting (PDR) method. PDR exhibits robust performance across four distinct systems, including a miniprotein, a cyclic peptide, a protein loop, and a protein-peptide complex. It accurately restores the conformational distributions at high temperatures to those at low temperatures. Additionally, we apply PDR to reweight previously studied high-T MD simulations of 12 protein-peptide complexes, enabling a comprehensive investigation of the conformational space of protein-peptide complexes.

Peptide diffusion in biomolecular condensates

Diffusion determines the turnover of biomolecules in liquid-liquid phase-separated condensates. We considered the mean square displacement and thus the diffusion constant for simple model systems of peptides GGGGG, GGQGG, and GGVGG in aqueous solutions after phase separation by simulating atomic-level models. These solutions readily separate into aqueous and peptide-rich droplet phases. We noted the effect of the peptides being in a solvated, surface, or droplet state on the peptide’s diffusion coefficients. Both sequence and peptide conformational distribution were found to influence diffusion and condensate turnover in these systems, with sequence dominating the magnitude of the differences. We found that the most compact structures for each sequence diffused the fastest in the peptide-rich condensate phase. This model result may have implications for turnover dynamics in signaling systems.

A high-resolution large-area detector for quality assurance in radiotherapy

Hadron therapy is an advanced radiation modality for treating cancer, which currently uses protons and carbon ions. Hadrons allow for a highly conformal dose distribution to the tumour, minimising the detrimental side-effects due to radiation received by healthy tissues. Treatment with hadrons requires sub-millimetre spatial resolution and high dosimetric accuracy. This paper discusses the design, fabrication and performance tests of a detector based on Gas Electron Multipliers (GEM) coupled to a matrix of thin-film transistors (TFT), with an active area of 60 × 80 mm2 and 200 ppi resolution. The experimental results show that this novel detector is able to detect low-energy (40 kVp X-rays), high-energy (6 MeV) photons used in conventional radiation therapy and protons and carbon ions of clinical energies used in hadron therapy. The GEM-TFT is a compact, fully scalable, radiation-hard detector that measures secondary electrons produced by the GEMs with sub-millimetre spatial resolution and a linear response for proton currents from 18 pA to 0.7 nA. Correcting known detector defects may aid in future studies on dose uniformity, LET dependence, and different gas mixture evaluation, improving the accuracy of QA in radiotherapy.

Dosimetric benefits and preclinical performance of steerable needles in HDR prostate brachytherapy

Prostate cancer patients with an enlarged prostate and/or excessive pubic arch interference (PAI) are generally considered non-eligible for high-dose-rate (HDR) brachytherapy (BT). Steerable needles have been developed to make these patients eligible again. This study aims to validate the dosimetric impact and performance of steerable needles within the conventional clinical setting.HDR BT treatment plans were generated, needle implantations were performed in a prostate phantom, with prostate volume > 55 cm3 and excessive PAI of 10 mm, and pre- and post-implant dosimetry were compared considering the dosimetric constraints: prostate V100 > 95 % (13.50 Gy), urethra D0.1cm3 < 115 % (15.53 Gy) and rectum D1cm3 < 75 % (10.13 Gy).The inclusion of steerable needles resulted in a notable enhancement of the dose distribution and prostate V100 compared to treatment plans exclusively employing rigid needles to address PAI. Furthermore, the steerable needle plan demonstrated better agreement between pre- and post-implant dosimetry (prostate V100: 96.24 % vs. 93.74 %) compared to the rigid needle plans (79.13 % vs. 72.86 % and 87.70 % vs. 81.76 %), with no major changes in the clinical workflow and no changes in the clinical set-up.The steerable needle approach allows for more flexibility in needle positioning, ensuring a highly conformal dose distribution, and hence, HDR BT is a feasible treatment option again for prostate cancer patients with an enlarged prostate and/or excessive PAI.

Controversies in neuro-oncology: Focal proton versus photon radiation therapy for adult brain tumors.

Radiation therapy (RT) plays a fundamental role in the treatment of malignant and benign brain tumors. Current state-of-the-art photon- and proton-based RT combines more conformal dose distribution of target volumes and accurate dose delivery while limiting the adverse radiation effects. PubMed was systematically searched from from 2000 to October 2023 to identify studies reporting outcomes related to treatment of central nervous system (CNS)/skull base tumors with PT in adults. Several studies have demonstrated that proton therapy (PT) provides a reduced dose to healthy brain parenchyma compared with photon-based (xRT) radiation techniques. However, whether dosimetric advantages translate into superior clinical outcomes for different adult brain tumors remains an open question. This review aims at critically reviewing the recent studies on PT in adult patients with brain tumors, including glioma, meningiomas, and chordomas, to explore its potential benefits compared with xRT.

Alchemical Enhanced Sampling with Optimized Phase Space Overlap.

An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate importance sampling in free energy simulations. The method achieves enhanced sampling from Hamiltonian replica exchange within a dual topology framework while utilizing new smoothstep softcore potentials. A common sampling problem encountered in lead optimization is the functionalization of aromatic rings that exhibit distinct conformational preferences when interacting with the protein. It is difficult to converge the distribution of ring conformations due to the long time scale of ring flipping events; however, the ACES method addresses this issue by modeling the syn and anti ring conformations within a dual topology. ACES thereby samples the conformer distributions by alchemically tunneling between states, as opposed to traversing a physical pathway with a high rotational barrier. We demonstrate the use of ACES to overcome conformational sampling issues involving ring flipping in ML300-derived noncovalent inhibitors of SARS-CoV-2 Main Protease (Mpro). The demonstrations explore how the use of replica exchange and the choice of softcore selection affects the convergence of the ring conformation distributions. Furthermore, we examine how the accuracy of the calculated free energies is affected by the degree of phase space overlap (PSO) between adjacent states (i.e., between neighboring λ-windows) and the Hamiltonian replica exchange acceptance ratios. Both of these factors are sensitive to the spacing between the intermediate states. We introduce a new method for choosing a schedule of λ values. The method analyzes short "burn-in" simulations to construct a 2D map of the nonlocal PSO. The schedule is obtained by optimizing an alchemical pathway on the 2D map that equalizes the PSO between the λ intervals. The optimized phase space overlap λ-spacing method (Opt-PSO) leads to more numerous end-to-end single passes and round trips due to the correlation between PSO and Hamiltonian replica exchange acceptance ratios. The improved exchange statistics enhance the efficiency of ACES method. The method has been implemented into the FE-ToolKit software package, which is freely available.