Detecting M-Protein via Mass Spectrometry and Affinity Beads: Enrichment With Mixed Kappa-Lambda Beads Enables Prompt Application in Clinical Laboratories.

Background: Detecting monoclonal protein (M-protein), a hallmark of plasma cell disorders, traditionally relies on methods such as protein electrophoresis, immune-electrophoresis, and immunofixation electrophoresis (IFE). Mass spectrometry (MS)-based methods, such as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization-quadrupole time-of-flight (ESI-qTOF) MS, have emerged as sensitive methods. We explored the M-protein-detection efficacies of different MS techniques. Methods: To isolate immunoglobulin and light chain proteins, six types of beads (IgG, IgA, IgM, kappa, lambda, and mixed kappa and lambda) were used to prepare samples along with CaptureSelect nanobody affinity beads (NBs). After purification, both MALDI-TOF MS and liquid chromatography coupled with Synapt G2 ESI-qTOF high-resolution MS analysis were performed. We purified 25 normal and 25 abnormal IFE samples using NBs and MALDI-TOF MS (NB-MALDI-TOF). Results: Abnormal samples showed monoclonal peaks, whereas normal samples showed polyclonal peaks. The IgG and mixed kappa and lambda beads showed monoclonal peaks following the use of daratumumab (an IgG/kappa type of monoclonal antibody) with both MALDI-TOF and ESI-qTOF MS analysis. The limits of detection for MALDI-TOF MS and ESI-qTOF MS were established as 0.1 g/dL and 0.025 g/dL, respectively. NB-MALDI-TOF and IFE exhibited comparable sensitivity and specificity (92% and 92%, respectively). Conclusions: NBs for M-protein detection, particularly with mixed kappa-lambda beads, identified monoclonal peaks with both MALDI-TOF and ESI-qTOF analyses. Qualitative analysis using MALDI-TOF yielded results comparable with that of IFE. NB-MALDI-TOF might be used as an alternative method to replace conventional tests (such as IFE) to detect M-protein with high sensitivity.

In vitro Evaluation of DINCH-Plasticized Blood Bags for Red Blood Cell Storage with CPDA-1 Anticoagulant.

Introduction: Di(2-ethylhexyl) phthalate (DEHP) is a plasticizer commonly used in blood bags. Despite its protective effects on red blood cell (RBC) storage, concerns about its reproductive toxicity exist. This study investigated the in vitro quality of RBC concentrates stored in bags using di(isononyl) cyclohexane-1,2-dicarboxylate (DINCH) as an alternative plasticizer. Methods: Using a pool-and-split study design, we produced 20 matched homogenous quintets of RBC concentrates in two DINCH bags and three DEHP bags with citrate phosphate dextrose adenine (CPDA-1) anticoagulant. RBC storage quality was assessed weekly for 35 days. Results: On day 35, the median hemolysis levels in the DINCH bags (0.297-0.342%) were marginally higher (p < 0.05) than the DEHP bags (0.204-0.240%). All DINCH bags showed <0.8% hemolysis. RBCs in the DINCH bags showed increased mean corpuscular volume and decreased eosin 5' maleimide binding than in the DEHP bags. Higher pO2 and lower pCO2 levels in the DINCH bags indicated better gas permeability than in DEHP bags. Other metabolic parameters were comparable in both bags. Compared to DEHP, DINCH exhibited considerably lower levels of plasticizer leaching into blood bags. Conclusion: The quality of RBC concentrates stored for 35 days in DINCH-plasticized blood bags with CDPA-1 is generally comparable to those in DEHP bags. Hence, DINCH can be a viable alternative to DEHP in blood bags for nonleukoreduced RBC storage even without the use of next-generation additive solutions to improve RBC preservation quality.

A plasticizer is a chemical substance added to plastic to increase its flexibility. DEHP is a plasticizer that has been widely used in many products including plastic tubing and bags of medical devices. However, concerns about DEHP-related toxicity have been debated for many years. DEHP has been replaced with other plasticizers in many products, but it is still being used in blood bags due to its protective effect on RBC preservation. DINCH is an alternative plasticizer with a low toxicology profile. This study investigated the quality of RBC concentrates stored in blood bags using DINCH. Twenty sets of five RBC concentrates were produced using two DINCH bags and three DEHP bags with CPDA-1 anticoagulant, and the storage quality was assessed weekly for 35 days. On day 35, the median hemolysis levels in the DINCH bags (0.297­0.342%) were slightly increased than the DEHP bags (0.204­0.240%). However, all DINCH bags showed hemolysis lower than the regulatory limit of 0.8%. DINCH bags exhibited better gas permeability than DEHP bags. Compared to DEHP, DINCH exhibited considerably lower levels of plasticizer leaching into blood bags. Most of the other metabolic parameters were comparable in both bags. The quality of nonleukocyte-reduced RBC concentrates stored for 35 days in DINCH-plasticized blood bags with CDPA-1 is generally comparable to those in DEHP bags. Hence, DINCH can be a viable alternative to DEHP in blood bags for RBC storage, even without the use of next-generation additive solutions to improve RBC preservation quality.

Drosophila HCN mediates gustatory homeostasis by preserving sensillar transepithelial potential in sweet environments.

Establishing transepithelial ion disparities is crucial for sensory functions in animals. In insect sensory organs called sensilla, a transepithelial potential, known as the sensillum potential (SP), arises through active ion transport across accessory cells, sensitizing receptor neurons such as mechanoreceptors and chemoreceptors. Because multiple receptor neurons are often co-housed in a sensillum and share SP, niche-prevalent overstimulation of single sensory neurons can compromise neighboring receptors by depleting SP. However, how such potential depletion is prevented to maintain sensory homeostasis remains unknown. Here, we find that the Ih-encoded hyperpolarization-activated cyclic nucleotide-gated (HCN) channel bolsters the activity of bitter-sensing gustatory receptor neurons (bGRNs), albeit acting in sweet-sensing GRNs (sGRNs). For this task, HCN maintains SP despite prolonged sGRN stimulation induced by the diet mimicking their sweet feeding niche, such as overripe fruit. We present evidence that Ih-dependent demarcation of sGRN excitability is implemented to throttle SP consumption, which may have facilitated adaptation to a sweetness-dominated environment. Thus, HCN expressed in sGRNs serves as a key component of a simple yet versatile peripheral coding that regulates bitterness for optimal food intake in two contrasting ways: sweet-resilient preservation of bitter aversion and the previously reported sweet-dependent suppression of bitter taste.

Quantitative Evaluation of the Real-World Harmonization Status of Laboratory Test Items Using External Quality Assessment Data.

Background: In recent decades, the analytical quality of clinical laboratory results has substantially increased because of collaborative efforts. To effectively utilize laboratory results in applications, such as machine learning through big data, understanding the level of harmonization for each test would be beneficial. We aimed to develop a quantitative harmonization index that reflects the harmonization status of real-world laboratory tests. Methods: We collected 2021-2022 external quality assessment (EQA) results for eight tests (HbA1c, creatinine, total cholesterol, HDL-cholesterol, triglyceride, alpha-fetoprotein [AFP], carcinoembryonic antigen [CEA], and prostate-specific antigen [PSA]). This EQA was conducted by the Korean Association of External Quality Assessment Service, using commutable materials. The total analytical error of each test was determined according to the bias% and CV% within peer groups. The values were divided by the total allowable error from biological variation (minimum, desirable, and optimal) to establish a real-world harmonization index (RWHI) at each level (minimum, desirable, and optimal). Good harmonization was arbitrarily defined as an RWHI value ≤ 1 for the three levels. Results: Total cholesterol, triglyceride, and CEA had an optimal RWHI of ≤ 1, indicating an optimal harmonization level. Tests with a desirable harmonization level included HDL-cholesterol, AFP, and PSA. Creatinine had a minimum harmonization level, and HbA1c did not reach the minimum harmonization level. Conclusions: We developed a quantitative RWHI using regional EQA data. This index may help reflect the actual harmonization level of laboratory tests in the field.

Thrombin Priming Promotes the Neuroprotective Effects of Human Wharton's Jelly-Derived Mesenchymal Stem Cells Via the HGF/AKT/STAT3 Signaling Pathway.

Mesenchymal stem cells (MSCs) directly differentiate into neurons and endothelial cells after transplantation, and their secretome has considerable potential for treating brain injuries. Previous studies have suggested that the effects of MSCs priming with exposure to hypoxia, cytokines, growth factors, or chemical agents could optimize the paracrine potency and therapeutic potential of MSCs. Studies have suggested that thrombin-primed Wharton's Jelly-derived mesenchymal stem cells (Th.WJ-MSCs) significantly enhance the neuroprotective beneficial effects of naive MSCs in brain injury such as hypoxic-ischemic brain injury (HIE) and intraventricular hemorrhage (IVH). This study aimed to characterize WJ-MSCs in terms of stem cell markers, differentiation, cell proliferation, and paracrine factors by comparing naive and Th.WJ-MSCs. We demonstrated that compared with naive MSCs, Th.MSCs significantly enhanced the neuroprotective effects in vitro. Moreover, we identified differentially expressed proteins in the conditioned media of naive and Th.WJ-MSCs by liquid chromatography-tandem mass spectrometry analysis. Secretome analysis of the conditioned medium of WJ-MSCs revealed that such neuroprotective effects were mediated by paracrine effects with secretomes of Th.WJ-MSCs, and hepatocyte growth factor was identified as a key paracrine mediator. These results can be applied further in the preclinical and clinical development of effective and safe cell therapeutics for brain injuries such as HIE and IVH.

Multicenter comparison of analytical interferences of 25-OH vitamin D immunoassay and mass spectrometry methods by endogenous interferents and cross-reactivity with 3-epi-25-OH-vitamin D3.

Background: Vitamin D (vit-D) deficiency is highly prevalent in the Korean population, highlighting the need for accurate measurements. In this study, the interferences by endogenous and cross-reactive substances were compared between routine vit-D immunoassays and mass spectrometry (MS) methods. Methods: Two MS methods and 4 immunoassays from different manufacturers (Abbott, Beckman Coulter, Roche, Siemens) were compared. Residual samples that were icteric, lipemic, hemolyzed, high in rheumatoid factor, from myeloma patients, or patients undergoing hemodialysis were collected. Also, 4 levels of National Institute of Standards and Technology (NIST) Standard Reference Material 972a, and 12 samples serially spiked with 3-epi-25-OH-D3 were prepared. Results: Significant interferences were observed in hemolytic (Roche), icteric (Beckman and Siemens) and lipemic samples (all 4 immunoassays). Level 4 NIST material and 3-epi-25-OH-D3-spiked samples induced significant cross-reactivity, yielding higher total vit-D measurements in non-epimer-separating MS methods, and both the Beckman and Roche immunoassays. Conclusion: Most observed interferences were consistent with manufacturers' claims, but overall improvement of immunoassay bias limits is required. Awareness of potential interference is important to increase the accuracy of vit-D measurements. Moreover, care is due when interpreting vit-D results of newborns, infants and less commonly, pregnant women, who are known to have physiologically high levels of the highly cross-reactive 3-epi-25-OH-D3.

Deep Learning-Based Chemical Similarity for Accelerated Organic Light-Emitting Diode Materials Discovery.

Thermally activated delayed fluorescence (TADF) material has attracted great attention as a promising metal-free organic light-emitting diode material with a high theoretical efficiency. To accelerate the discovery of novel TADF materials, computer-aided material design strategies have been developed. However, they have clear limitations due to the accessibility of only a few computationally tractable properties. Here, we propose TADF-likeness, a quantitative score to evaluate the TADF potential of molecules based on a data-driven concept of chemical similarity to existing TADF molecules. We used a deep autoencoder to characterize the common features of existing TADF molecules with common chemical descriptors. The score was highly correlated with the four essential electronic properties of TADF molecules and had a high success rate in large-scale virtual screening of millions of molecules to identify promising candidates at almost no cost, validating its feasibility for accelerating TADF discovery. The concept of TADF-likeness can be extended to other fields of materials discovery.

Revealing Two Distinct Formation Pathways of 2D Wurtzite-CdSe Nanocrystals Using In Situ X-Ray Scattering.

Understanding the mechanism underlying the formation of quantum-sized semiconductor nanocrystals is crucial for controlling their synthesis for a wide array of applications. However, most studies of 2D CdSe nanocrystals have relied predominantly on ex situ analyses, obscuring key intermediate stages and raising fundamental questions regarding their lateral shapes. Herein, the formation pathways of two distinct quantum-sized 2D wurtzite-CdSe nanocrystals - nanoribbons and nanosheets - by employing a comprehensive approach, combining in situ small-angle X-ray scattering techniques with various ex situ characterization methods is studied. Although both nanostructures share the same thickness of ≈1.4 nm, they display contrasting lateral dimensions. The findings reveal the pivotal role of Se precursor reactivity in determining two distinct synthesis pathways. Specifically, highly reactive precursors promote the formation of the nanocluster-lamellar assemblies, leading to the synthesis of 2D nanoribbons with elongated shapes. In contrast, mild precursors produce nanosheets from a tiny seed of 2D nuclei, and the lateral growth is regulated by chloride ions, rather than relying on nanocluster-lamellar assemblies or Cd(halide)2 -alkylamine templates, resulting in 2D nanocrystals with relatively shorter lengths. These findings significantly advance the understanding of the growth mechanism governing quantum-sized 2D semiconductor nanocrystals and offer valuable guidelines for their rational synthesis.

DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening.

Recently emerging generative AI models enable us to produce a vast number of compounds for potential applications. While they can provide novel molecular structures, the synthetic feasibility of the generated molecules is often questioned. To address this issue, a few recent studies have attempted to use deep learning models to estimate the synthetic accessibility of many molecules rapidly. However, retrosynthetic analysis tools used to train the models rely on reaction templates automatically extracted from a large reaction database that are not domain-specific and may exhibit low chemical correctness. To overcome this limitation, we introduce DFRscore (Drug-Focused Retrosynthetic score), a deep learning-based approach for a more practical assessment of synthetic accessibility in drug discovery. The DFRscore model is trained exclusively on drug-focused reactions, providing a predicted number of minimally required synthetic steps for each compound. This approach enables practitioners to filter out compounds that do not meet their desired level of synthetic accessibility at an early stage of high-throughput virtual screening for accelerated drug discovery. The proposed strategy can be easily adapted to other domains by adjusting the synthesis planning setup of the reaction templates and starting materials.

Optimizing Contact Between Older Adults and Senior Services: South Korean users' Perceptions of Gateway Institutions.

In response to the growing need for effective policy implementation strategies for older adults in South Korea, we propose the establishment of a user-centered institution tightly integrated with policies, termed, "comprehensive gateway institution for older adults." This research addresses the challenges 231 older adult users face when navigating various health policies. Our survey findings revealed that these users experienced difficulties in dealing with the current policy approach for older adults. The respondents expressed their expectations for improved service access through the proposed gateway institution. They emphasized the importance of universal access to services and the need for personalized offerings that consider their unique circumstances, physical abilities, and skills. By incorporating these research outcomes into practice, we can help lay the groundwork for more effective policies measures and create a system that better meets the needs of older adults in the future.

Critical role of electrons in the short lifetime of blue OLEDs.

Designing robust blue organic light-emitting diodes is a long-standing challenge in the display industry. The highly energetic states of blue emitters cause various degradation paths, leading to collective luminance drops in a competitive manner. However, a key mechanism of the operational degradation of organic light-emitting diodes has yet to be elucidated. Here, we show that electron-induced degradation reactions play a critical role in the short lifetime of blue organic light-emitting diodes. Our control experiments demonstrate that the operational lifetime of a whole device can only be explained when excitons and electrons exist together. We examine the atomistic mechanisms of the electron-induced degradation reactions by analyzing their energetic profiles using computational methods. Mass spectrometric analysis of aged devices further confirm the key mechanisms. These results provide new insight into rational design of robust blue organic light-emitting diodes.

Layer-Dependent Interaction Effects in the Electronic Structure of Twisted Bilayer Graphene Devices.

Near the magic angle, strong correlations drive many intriguing phases in twisted bilayer graphene (tBG) including unconventional superconductivity and chern insulation. Whether correlations can tune symmetry breaking phases in tBG at intermediate (≳ 2°) twist angles remains an open fundamental question. Here, using ARPES, we study the effects of many-body interactions and displacement field on the band structure of tBG devices at an intermediate (3°) twist angle. We observe a layer- and doping-dependent renormalization of bands at the K points that is qualitatively consistent with moiré models of the Hartree-Fock interaction. We provide evidence of correlation-enhanced inversion symmetry-breaking, manifested by gaps at the Dirac points that are tunable with doping. These results suggest that electronic interactions play a significant role in the physics of tBG even at intermediate twist angles and present a new pathway toward engineering band structure and symmetry-breaking phases in moiré heterostructures.

Evaluation of Vancomycin TDM Strategies: Prediction and Prevention of Kidney Injuries Based on Vancomycin TDM Results.

The current guidelines for therapeutic drug monitoring (TDM) of vancomycin suggest a target 24-hour area under the curve (AUC0-24) of 400 to 600 mg*h/L for serious methicillin-resistant Staphylococcus aureus infections. In this study, the predictabilities of acute kidney injury (AKI) of various TDM target parameters, target levels, and sampling methods were evaluated in patients who underwent TDM from January 2020 to December 2020. The AUC0-24 and trough values were calculated by both one- and two-point sampling methods, and were evaluated for the predictability of AKI. Among the AUC0-24 cutoff comparisons, the threshold value of 500 mg*h/L in the two sampling methods was statistically significant (P = 0.042) when evaluated for the predictability of AKI. Analysis by an receiver operating characteristic curve estimated an AUC0-24 cutoff value of 563.45 mg*h/L as a predictor of AKI, and was proposed as the upper limit of TDM target.

Comparison of two highly sensitive benzodiazepine immunoassay lab developed tests for urine drug testing in clinical specimens.

Background: The VALID Act is a legislative effort that, if enacted, would alter the regulatory requirements of laboratory developed tests (LDTs) used for clinical testing in the United States. Benzodiazepines, which are primarily excreted into urine as glucuronidated metabolites such as lorazepam, cross-react poorly with FDA-cleared immunoassays, leading to false-negatives. This shortfall can be addressed with LDTs created by adding glucuronidase to the immunoassay reagents producing "high sensitivity" assays that detect glucuronidated metabolites. Methods: Precision and stability of two high-sensitivity (HS) benzodiazepine immunoassays from Roche and Thermo Scientific were evaluated using manufacturer-supplied quality control (QC) material and glucuronidated QC material. The immunoassays were directly compared to an LC-MS/MS LDT benzodiazepine assay to determine clinical sensitivity/specificity using urine specimens (n = 82 for Thermo Scientific; n = 265 for Roche). The clinical impact of the HS LDT immunoassay was determined by analyzing clinical testing results 60 days before and after its implementation. Results: The precision and clinical sensitivity/specificity of the HS-Thermo Scientific and HS-Roche benzodiazepine assays were acceptable. The reagent stability of the HS-Thermo Scientific immunoassay was poor, whereas the HS-Roche immunoassay was stable. After implementation of the HS-Roche benzodiazepine immunoassay as an LDT, there was a 30-fold increase (p-value: < 0.00001) in the percentage of lorazepam confirmations. Conclusions: We demonstrate the development and validation of an immunoassay LDT with improved sensitivity for glucuronidated benzodiazepines. This LDT can detect glucuronidated benzodiazepines in clinical urine specimens and is stable for 60 days. Importantly, we were able to validate the immunoassay as an LDT by utilizing an LC-MS/MS LDT.

Serum Vitamin D Level Correlations With Tissue Vitamin D Level and Muscle Performance Before and After Rotator Cuff Repair.

BACKGROUND: There is a lack of studies about serum and tissue vitamin D levels of the rotator cuff muscle on muscle power, fatty degeneration, and healing failure after rotator cuff repair (RCR). Furthermore, no studies have evaluated vitamin D receptor proteins in the rotator cuff that show a close association with serum vitamin D levels. PURPOSE: To evaluate the correlations between serum vitamin D and tissue vitamin D as well as perioperative variables of arthroscopic RCR. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: From March 2017 to October 2017, a total of 36 patients who underwent RCR were prospectively enrolled, and supraspinatus muscle tissue was obtained during surgery to analyze tissue vitamin D levels. Serum vitamin D levels were checked preoperatively and at 6 months and 1 year postoperatively. Tissue vitamin D levels were assessed using liquid chromatography, and the vitamin D receptor was measured by western blotting. Isokinetic muscle performance test (IMPT; peak torque and torque deficiency compared with the opposite shoulder) results and fatty degeneration of the rotator cuff using the Goutallier classification were assessed preoperatively and at 1 year after surgery. The American Shoulder and Elbow Surgeons score and Constant score were collected at 2 years after surgery. Healing failure of the repaired rotator cuff was analyzed by magnetic resonance imaging at 1 year after surgery. RESULTS: Overall, only three patients (8.3%) had serum vitamin D sufficiency (>20 ng/mL). Among 36 patients, 26 patients returned for their 1-year follow-up. Lower preoperative serum vitamin D levels resulted in lower serum vitamin D levels at 6 months and 1 year postoperatively (all P < .05). Lower preoperative and 1-year postoperative serum vitamin D levels resulted in more torque deficiency on the IMPT in abduction than higher preoperative and 1-year postoperative serum vitamin D levels (all P < .05). Tissue vitamin D levels had a strong correlation with preoperative serum vitamin D levels (P = .001). Lower tissue vitamin D levels were associated with lower peak torque on the IMPT in abduction (P = .043) and a tendency of lower peak torque on the IMPT in external rotation (P = .077) at 1 year postoperatively. There was no correlation between tissue and serum vitamin D levels and functional outcomes, fatty degeneration, and healing failure after surgery (all P > .05). The vitamin D receptor showed no correlation with any variables (all P > .05). CONCLUSION: Lower preoperative serum vitamin D levels had a strong correlation with lower tissue vitamin D levels and lower serum vitamin D levels at 1 year after surgery. Furthermore, the patients with lower serum vitamin D levels showed more weakness of muscle power perioperatively. The results of this study emphasized the association between vitamin D levels and rotator cuff muscle power.

Effect of alanine versus serine at position 88 of human transthyretin mutants on the protein stability.

Human transthyretin (TTR) is a homo-tetrameric plasma protein associated with a high percentage of ß-sheet forming amyloid fibrils. It accumulates in tissues or extracellular matrices to cause amyloid diseases. Free energy simulations with thermodynamic integration based on all-atom molecular dynamics simulations have been carried out to analyze the effects of the His88 â†’ Ala and Ser mutations on the stability of human TTR. The calculated free energy change differences (ΔΔG) caused by the His88 â†’ Ala and His88 â†’ Ser mutations are -1.84 ± 0.86 and 7.56 ± 0.55 kcal/mol, respectively, which are in excellent agreement with prior reported experimental values. The simulation results show that the H88A mutant is more stable than the wild type, whereas the H88S mutant is less stable than the wild type. The free energy component analysis shows that the contribution to the free energy change difference (ΔΔG) for the His88 â†’ Ala and His88 â†’ Ser mutations mainly arise from electrostatic and van der Waals interactions, respectively. The electrostatic term stabilizes the H88A mutant more than the wild type, but the van der Waals interaction destabilizes the H88S mutant relative to the wild type. Individual residue contributions to the free energy change show neighboring residues exert stabilizing and destabilizing influence on the mutants. The implications of the simulation results for understanding the stabilizing and destabilizing effect and its contribution to protein stability are discussed.

Free energy simulations to study mutational effect of a conserved residue, Trp24, on stability of human serum retinol-binding protein.

Human serum retinol-binding protein (RBP) is a plasma transport protein for vitamin A. RBP is a prime subclass of lipocalins, which bind nonpolar ligands within a ß-barrel. To understand the role of Trp 24, one of the highly conserved residues in RBP, free energy simulations have been carried out to understand the effects of the mutations from Trp at position 24 to Leu, Phe, and Tyr in the apo-RBP on its thermal stability. We examine various unfolded systems to study the dependence of the free energy differences on the denatured structure. Our calculated free energy difference values for the three mutations are in excellent agreement with the experimental values when the initial coordinates of the seven-residue peptide segments truncated from the crystal structure are used for the denatured systems. Our free energy change differences for the Trp→Leu, Trp→Phe, and Trp→Tyr mutations are 2.50 ± 0.69, 2.58 ± 0.50, and 2.49 ± 0.48 kcal/mol, respectively, when the native-like seven-residue peptides are used as models for the denatured systems. The main contributions to the free energy change differences for the Trp24→Leu and Trp24→Phe mutations are mainly from van der Waals and covalent interactions, respectively. Electrostatic, van der Waals and covalent terms equally contribute to the free energy change difference for the Trp24→Tyr mutation. The free energy simulation helps understand the detailed microscopic mechanism of the stability of the RBP mutants relative to the wild type and the role of the highly conserved residue, Trp24, of the human RBP.Communicated by Ramaswamy H. Sarma.

Simulation analysis of selective alanine mutation effect on stability of human prion protein.

Prion diseases are neurodegenerative disorders caused by spongiform degeneration of the brain. Understanding the fundamental mechanism of prion protein aggregation caused by mutations is very crucial to resolve the pathology of prion diseases. To help understand the roles of individual residues on the stability of the human prion protein, the computational method of free energy simulations based on atomistic molecular dynamics trajectories is applied to Phe175 → Ala, Val180 → Ala, and Val209 → Ala mutations of the human prion protein. The simulations show that all three alanine mutations destabilize the human prion protein. The calculated free energy change differences, ΔΔG, for the Phe175 → Ala, Val180 → Ala, and Val209 → Ala mutations are in good agreement with the experimental values. The significant destabilizing effects on the mutants relative to the wild-type protein arise from van der Waals terms. Furthermore, our free energy decomposition analysis shows that the major contribution to destabilizing the V180A and V209A mutants relative to the wild-type protein is originated from van der Waals interactions from residues near the mutation sites. In contrast, the contribution to destabilizing the F175A mutant is mainly caused by van der Waals interactions from residues near and far away from the mutation site. Our results show that the free energy simulation with a thermodynamic integration approach for selected alanine scanning mutations is beneficial for understanding the detailed mechanism of human prion protein destabilization, specific residues' role, and the hydrophobic effect on protein stability.Communicated by Ramaswamy H. Sarma.