A novel approach to study multi-domain motions in JAK1's activation mechanism based on energy landscape.

The family of Janus Kinases (JAKs) associated with the JAK-signal transducers and activators of transcription signaling pathway plays a vital role in the regulation of various cellular processes. The conformational change of JAKs is the fundamental steps for activation, affecting multiple intracellular signaling pathways. However, the transitional process from inactive to active kinase is still a mystery. This study is aimed at investigating the electrostatic properties and transitional states of JAK1 to a fully activation to a catalytically active enzyme. To achieve this goal, structures of the inhibited/activated full-length JAK1 were modelled and the energies of JAK1 with Tyrosine Kinase (TK) domain at different positions were calculated, and Dijkstra's method was applied to find the energetically smoothest path. Through a comparison of the energetically smoothest paths of kinase inactivating P733L and S703I mutations, an evaluation of the reasons why these mutations lead to negative or positive regulation of JAK1 are provided. Our energy analysis suggests that activation of JAK1 is thermodynamically spontaneous, with the inhibition resulting from an energy barrier at the initial steps of activation, specifically the release of the TK domain from the inhibited Four-point-one, Ezrin, Radixin, Moesin-PK cavity. Overall, this work provides insights into the potential pathway for TK translocation and the activation mechanism of JAK1.

Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.

Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions that are bound or restricted at the Ncd-tubulin dimer binding interfaces. To consider the ion effects, widely used implicit solvent models treat ions implicitly in the continuous solvent environment without focusing on the individual ions' effects. But highly charged biomolecules such as the Ncd and tubulin dimer may capture some ions at highly charged regions as bound ions. Such bound ions are restricted to their binding sites; thus, they can be treated as part of the biomolecules. By applying multiscale computational methods, including the machine-learning-based Hybridizing Ions Treatment-2 program, molecular dynamics simulations, DelPhi, and DelPhiForce, we studied the interaction between the Ncd motor domain and the tubulin dimer using a hybrid solvent model, which considers the bound ions explicitly and the other ions implicitly in the solvent environment. To identify the importance of treating bound ions explicitly, we also performed calculations using the implicit solvent model without considering the individual bound ions. We found that the calculations of the electrostatic features differ significantly between those of the hybrid solvent model and the pure implicit solvent model. The analyses show that treating bound ions at highly charged regions explicitly is crucial for electrostatic calculations. This work proposes a machine-learning-based approach to handle the bound ions using the hybrid solvent model. Such an approach is not only capable of handling kinesin-tubulin complexes but is also appropriate for other highly charged biomolecules, such as DNA/RNA, viral capsid proteins, etc.

Preparing for parenthood: Validating a mixed method approach to assessing the coparenting capacity of young expectant fathers and mothers.

The transition to parenthood (TP) interview and coparenting capacity (CC) coding scheme is a mixed method approach to evaluating readiness for the interpersonal challenges of parenthood. This paper focuses on the validation of the TP-CC system with a diverse sample of 140 young expectant father/mother pairs. The TP interview is designed to assist expectant parents in expressing their thoughts and feelings about parenthood and coparenting and the CC coding scheme is designed to assess a new parent's capacity for expressing fondness, acceptance, growth, cohesion, and commitment in their relationship with their coparenting partner. Convergent validation of the TP-CC system involved measuring self- and partner-reported relationship quality, relationship security, and observed warmth and hostility during the pregnancy. Predictive validation focused on the same set of variables, measured at the 6-month postbirth follow-up. Results supported the convergent validity of the TP-CC system for mothers and fathers, with higher-specific CC scores correlating with higher relationship quality, relationship security and warmth scores, as well as lower hostility scores. Results partially supported predictive validity, with fathers' total CC scores predicting fathers' interpersonal hostility and mothers' relationship quality, relationship security, hostility, and warmth at follow-up. Consistently positive and significant correlations between both mothers and fathers prebirth and postbirth CC scores provide evidence for the test-retest reliability of the TP-CC system. Generally, findings demonstrate the potential utility of the TP-CC system for evaluating coparenting readiness across the transition to parenthood.

Acetate, a Short-Chain Fatty Acid, Acutely Lowers Heart Rate and Cardiac Contractility Along with Blood Pressure.

Short-chain fatty acids (SCFAs) are metabolites produced almost exclusively by the gut microbiota and are an essential mechanism by which gut microbes influence host physiology. Given that SCFAs induce vasodilation, we hypothesized that they might have additional cardiovascular effects. In this study, novel mechanisms of SCFA action were uncovered by examining the acute effects of SCFAs on cardiovascular physiology in vivo and ex vivo. Acute delivery of SCFAs in conscious radiotelemetry-implanted mice results in a simultaneous decrease in both mean arterial pressure and heart rate (HR). Inhibition of sympathetic tone by the selective ß-1 adrenergic receptor antagonist atenolol blocks the acute drop in HR seen with acetate administration, yet the decrease in mean arterial pressure persists. Treatment with tyramine, an indirect sympathomimetic, also blocks the acetate-induced acute drop in HR. Langendorff preparations show that acetate lowers HR only after long-term exposure and at a smaller magnitude than seen in vivo. Pressure-volume loops after acetate injection show a decrease in load-independent measures of cardiac contractility. Isolated trabecular muscle preparations also show a reduction in force generation upon SCFA treatment, though only at supraphysiological concentrations. These experiments demonstrate a direct cardiac component of the SCFA cardiovascular response. These data show that acetate affects blood pressure and cardiac function through parallel mechanisms and establish a role for SCFAs in modulating sympathetic tone and cardiac contractility, further advancing our understanding of the role of SCFAs in blood pressure regulation. SIGNIFICANCE STATEMENT: Acetate, a short-chain fatty acid, acutely lowers heart rate (HR) as well as mean arterial pressure in vivo in radiotelemetry-implanted mice. Acetate is acting in a sympatholytic manner on HR and exerts negative inotropic effects in vivo. This work has implications for potential short-chain fatty acid therapeutics as well as gut dysbiosis-related disease states.

BiasNet: A Model to Predict Ligand Bias Toward GPCR Signaling.

Signaling bias is a feature of many G protein-coupled receptor (GPCR) targeting drugs with potential clinical implications. Whether it is therapeutically advantageous for a drug to be G protein biased or ß-arrestin biased depends on the context of the signaling pathway. Here, we explored GPCR ligands that exhibit biased signaling to gain insights into scaffolds and pharmacophores that lead to bias. More specifically, we considered BiasDB, a database containing information about GPCR biased ligands, and focused our analysis on ligands which show either a G protein or ß-arrestin bias. Five different machine learning models were trained on these ligands using 15 different sets of features. Molecular fragments which were important for training the models were analyzed. Two of these fragments (number of secondary amines and number of aromatic amines) were more prevalent in ß-arrestin biased ligands. After training a random forest model on HierS scaffolds, we found five scaffolds, which demonstrated G protein or ß-arrestin bias. We also conducted t-SNE clustering, observing correspondence between unsupervised and supervised machine learning methods. To increase the applicability of our work, we developed a web implementation of our models, which can predict bias based on user-provided SMILES, drug names, or PubChem CID. Our web implementation is available at: drugdiscovery.utep.edu/biasnet.

Characterizing novel olfactory receptors expressed in the murine renal cortex.

The kidney uses specialized G protein-coupled receptors, including olfactory receptors (ORs), to act as sensors of molecules and metabolites. In the present study, we cloned and studied seven renal ORs, which we previously found to be expressed in the murine renal cortex. As most ORs are orphan receptors, our goal was to identify ligands for these ORs in the hope that this will guide future research into their functional roles. We identified novel ligands for two ORs: Olfr558 and Olfr90. For Olfr558, we confirmed activation by previously reported ligands and identified 16 additional carboxylic acids that activated this OR. The strongest activation of Olfr558 was produced by butyric, cyclobutanecarboxylic, isovaleric, 2-methylvaleric, 3-methylvaleric, 4-methylvaleric, and valeric acids. The primary in vivo source of both butyric and isovaleric acids is gut microbial metabolism. We also identified 14 novel ligands that activated Olfr90, the strongest of which were 2-methyl-4-propyl-1,3-oxathiane, 1-octen-3-ol, 2-octanol, and 3-octanol. Interestingly, 8 of these 14 ligands are of fungal origin. We also investigated the tissue distribution of these receptors and found that they are each found in a subset of "nonsensory" tissues. Finally, we examined the putative human orthologs of Olfr558 and Olfr90 and found that the human ortholog of Olfr558 (OR51E1) has a similar ligand profile, indicating that the role of this OR is likely evolutionarily conserved. In summary, we examined seven novel renal ORs and identified new ligands for Olfr558 and Olfr90, which imply that both of these receptors serve to detect metabolites produced by microorganisms.

A randomized trial of culturally accommodated versus standard group treatment for Latina/o adolescents with substance use disorders: Posttreatment through 12-month outcomes.

OBJECTIVES: Latina/o adolescents are at particular risk for substance use disorders (SUDs) and effective treatments are needed. Some critics indicate that standard evidence-based treatments may not meet the needs of Latina/o adolescents and culturally accommodated treatments are needed; however, few comparative studies have been conducted to test this assumption. This randomized trial was designed to test a standard group-based version of a cognitive-behavioral treatment (S-CBT) against its culturally accommodated equivalent (A-CBT) for a sample of Latina/o adolescents with SUDs. METHOD: Seventy Latina/o adolescents were randomly assigned to 1 of 2 treatment conditions and followed over 4 posttreatment time points with the last at 12-months. Generalized longitudinal mixed models for count data were conducted to evaluate treatment differences across time for adolescent substance use. The cultural variables ethnic identity, acculturation, and familism were included in the analysis as potential moderators of treatment outcome. RESULTS: A significant difference was found at the 12-month follow-up in favor of the culturally accommodated treatment (d = .92, 95% confidence interval, CI [.43, 1.42]) and parental familism moderated treatment outcome (d = .60, 95% CI [.12, 1.08]). CONCLUSION: This is one of the first studies to demonstrate that a culturally accommodated treatment differentially improved outcomes compared with that of its standard equivalent for a sample of Latina/o adolescents with SUDs. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Resurgent sodium current promotes action potential firing in the avian auditory brainstem.

KEY POINTS: Auditory brainstem neurons of all vertebrates fire phase-locked action potentials (APs) at high rates with remarkable fidelity, a process controlled by specialized anatomical and biophysical properties. This is especially true in the avian nucleus magnocellularis (NM) - the analogue of the mammalian anteroventral cochlear nucleus. In addition to high voltage-activated potassium (KHVA ) channels, we report, using whole cell physiology and modelling, that resurgent sodium current (INaR ) of sodium channels (NaV ) is equally important and operates synergistically with KHVA channels to enable rapid AP firing in NM. Anatomically, we detected strong NaV 1.6 expression near hearing maturation, which was less distinct during hearing development despite functional evidence of INaR , suggesting that multiple NaV channel subtypes may contribute to INaR . We conclude that INaR plays an important role in regulating rapid AP firing for NM neurons, a property that may be evolutionarily conserved for functions related to similar avian and mammalian hearing. ABSTRACT: Auditory brainstem neurons are functionally primed to fire action potentials (APs) at markedly high rates in order to rapidly encode the acoustic information of sound. This specialization is critical for survival and the comprehension of behaviourally relevant communication functions, including sound localization and distinguishing speech from noise. Here, we investigated underlying ion channel mechanisms essential for high-rate AP firing in neurons of the chicken nucleus magnocellularis (NM) - the avian analogue of bushy cells of the mammalian anteroventral cochlear nucleus. In addition to the established function of high voltage-activated potassium channels, we found that resurgent sodium current (INaR ) plays a role in regulating rapid firing activity of late-developing (embryonic (E) days 19-21) NM neurons. INaR of late-developing NM neurons showed similar properties to mammalian neurons in that its unique mechanism of an 'open channel block state' facilitated the recovery and increased the availability of sodium (NaV ) channels after depolarization. Using a computational model of NM neurons, we demonstrated that removal of INaR reduced high-rate AP firing. We found weak INaR during a prehearing period (E11-12), which transformed to resemble late-developing INaR properties around hearing onset (E14-16). Anatomically, we detected strong NaV 1.6 expression near maturation, which became increasingly less distinct at hearing onset and prehearing periods, suggesting that multiple NaV channel subtypes may contribute to INaR during development. We conclude that INaR plays an important role in regulating rapid AP firing for NM neurons, a property that may be evolutionarily conserved for functions related to similar avian and mammalian hearing.

Cultural accommodation of group substance abuse treatment for Latino adolescents: Results of an RCT.

Comparative studies examining the difference between empirically supported substance abuse treatments versus their culturally accommodated counterparts with participants from a single ethnic minority group are frequently called for in the literature but infrequently conducted in practice. This randomized clinical trial was conducted to compare the efficacy of an empirically supported standard version of a group-based cognitive-behavioral treatment (S-CBT) to a culturally accommodated version (A-CBT) with a sample of Latino adolescents primarily recruited from the juvenile justice system. Development of the culturally accommodated treatment and testing was guided by the Cultural Accommodation Model for Substance Abuse Treatment (CAM-SAT). Seventy Latino adolescents (mean age = 15.2; 90% male) were randomly assigned to 1 of 2 group-based treatment conditions (S-CBT = 36; A-CBT = 34) with assessments conducted at pretreatment, posttreatment, and 3-month follow-up. Longitudinal Poisson mixed models for count data were used to conduct the major analyses. The primary outcome variable in the analytic models was the number of days any substance was used (including alcohol, except tobacco) in the past 90 days. In addition, the variables ethnic identity, familism, and acculturation were included as cultural moderators in the analysis. Although both conditions produced significant decreases in substance use, the results did not support a time by treatment condition interaction; however, outcomes were moderated by ethnic identity and familism. The findings are discussed with implications for research and practice within the context of providing culturally relevant treatment for Latino adolescents with substance use disorders.

Measuring ethnic identity in Latino adolescents with substance use disorders.

The Multigroup Ethnic Identity Measure (MEIM) is a frequently used instrument to assess the level of ethnic identity in adolescents. The factor structure of the MEIM has extensively been studied in diverse nonclinical samples, while research with clinical samples of adolescents is lacking. The purpose of the current study is to identify the factor structure of the MEIM in a clinical sample of Latino adolescents (N = 106) with substance use disorders. A confirmatory factor analysis was used to test three competing factor structure models of the MEIM. Results indicated that a six-item two-factor model best fit the data for Latino adolescents in this study. Implications of these results and suggestions for further research are discussed.

Effects of Temporal Processing on Speech-in-Noise Perception in Middle-Aged Adults.

Auditory temporal processing is a vital component of auditory stream segregation, or the process in which complex sounds are separated and organized into perceptually meaningful objects. Temporal processing can degrade prior to hearing loss, and is suggested to be a contributing factor to difficulties with speech-in-noise perception in normal-hearing listeners. The current study tested this hypothesis in middle-aged adults-an under-investigated cohort, despite being the age group where speech-in-noise difficulties are first reported. In 76 participants, three mechanisms of temporal processing were measured: peripheral auditory nerve function using electrocochleography, subcortical encoding of periodic speech cues (i.e., fundamental frequency; F0) using the frequency following response, and binaural sensitivity to temporal fine structure (TFS) using a dichotic frequency modulation detection task. Two measures of speech-in-noise perception were administered to explore how contributions of temporal processing may be mediated by different sensory demands present in the speech perception task. This study supported the hypothesis that temporal coding deficits contribute to speech-in-noise difficulties in middle-aged listeners. Poorer speech-in-noise perception was associated with weaker subcortical F0 encoding and binaural TFS sensitivity, but in different contexts, highlighting that diverse aspects of temporal processing are differentially utilized based on speech-in-noise task characteristics.

Revisiting the Chicken Auditory Brainstem Response: Frequency Specificity, Threshold Sensitivity, and Cross Species Comparison.

The auditory brainstem response (ABR) is important for both clinical and basic auditory research. It is a non-invasive measure of hearing function with millisecond-level precision. The ABR can not only measure the synchrony, speed, and efficacy of auditory physiology but also detect different modalities of hearing pathology and hearing loss. ABRs are easily acquired in vertebrate animal models like reptiles, birds, and mammals, and complement existing molecular, developmental, and systems-level research. One such model system is the chicken; an excellent animal for studying auditory development, structure, and function. However, the ABR for chickens was last reported nearly 4 decades ago. The current study examines how decades of ABR characterization in other animal species support findings from the chicken ABR. We replicated and expanded on previous research using 43 chicken hatchlings 1- and 2-day post-hatch. We report that click-evoked chicken ABRs presented with a peak waveform morphology, amplitude, and latency like previous avian studies. Tone-evoked ABRs were found for frequencies from 250 to 4000 Hertz (Hz) and exhibited a range of best sensitivity between 750 and 2000 Hz. Objective click-evoked and tone-evoked ABR thresholds were comparable to subjective thresholds. With these revisited measurements, the chicken ABR still proves to be an excellent example of precocious avian development that complements decades of molecular, neuronal, and systems-level research in the same model organism.

Endocrinopathies in a Pediatric Patient Post-anatomical Hemispherectomy for Rasmussen's Encephalitis Treatment: A Case Report.

Hemispherectomy is a neurosurgical procedure that is frequently performed in pediatric patients diagnosed with Rasmussen's encephalitis. Postoperative complications include immediate complications such as hydrocephalus and hemorrhage and behavioral complications such as language impairments and contralateral weakness. However, there are limited studies or case reports that address the potential endocrinopathies associated with this and other pediatric epileptic surgeries. This case report describes the endocrinopathies following an anatomical hemispherectomy procedure. A four-year-old African-American female had a right anatomical hemispherectomy for the treatment of Rasmussen's encephalitis in 2020. The postoperative course was immediately complicated by central diabetes insipidus which was stabilized with desmopressin. The patient's labs in 2021 were consistent with central precocious puberty with elevated luteinizing hormone (LH) and follicle-stimulating hormone (FSH). Additionally, the patient was found to have secondary adrenal insufficiency in which she failed a low-dose adrenocorticotropic hormone (ACTH) stimulation test. Oral hydrocortisone therapy was initiated for secondary adrenal insufficiency in addition to initiating leuprolide injections for central precocious puberty. Furthermore, at the age of seven years, the patient had her first menarche. This case report emphasizes the need for closer and long-term surveillance for endocrine issues in postepileptic surgical pediatric patients as well as a surveillance plan for the development of other potential endocrine abnormalities throughout the patient's life.

How does the ion concentration affect the functions of kinesin BimC.

BimC family proteins are bipolar motor proteins belonging to the kinesin superfamily which promote mitosis by crosslinking and sliding apart antiparallel microtubules. Understanding the binding mechanism between the kinesin and the microtubule is crucial for researchers to make advances in the treatment of cancer and other malignancies. Experimental research has shown that the ion concentration affects the function of BimC significantly. But the insights of the ion-dependent function of BimC remain unclear. By combining molecular dynamics (MD) simulations with a series of computational approaches, we studied the electrostatic interactions at the binding interfaces of BimC and the microtubule under different KCl concentrations. We found the electrostatic interaction between BimC and microtubule is stronger at 0 mM KCl compared to 150 mM KCl, which is consistent with experimental conclusions. Furthermore, important salt bridges and residues at the binding interfaces of the complex were identified, which illustrates the details of the BimC-microtubule interactions. Molecular dynamics analyses of salt bridges identified that the important residues on the binding interface of BimC are positively charged, while those residues on the binding interface of the tubulin heterodimer are negatively charged. The finding in this work reveals some important mechanisms of kinesin-microtubule binding, which helps the future drug design for cancer therapy.

A Male Patient Presents With Isolated Abducens Nerve Palsy: An Atypical Presentation of Ocular Myasthenia Gravis.

Myasthenia gravis is an autoimmune disease of the neuromuscular junction caused by autoantibodies directed against the acetylcholine receptors. It presents with skeletal muscle weakness, often initially presenting with ocular symptoms such as ptosis and diplopia. When myasthenia gravis is isolated to only ocular symptoms, it is referred to as ocular myasthenia gravis (OMG). Here, we present an atypical initial presentation of OMG in a 68-year-old male patient presenting with isolated abducens nerve palsy at the initial onset. With this case report, we highlight the importance of a thorough history and clinical assessment necessary for a timely diagnosis of OMG in patients who present with isolated abducens nerve palsy.

TrkB downregulation is required for dendrite retraction in developing neurons of chicken nucleus magnocellularis.

The chick embryo (Gallus domesticus) is one of the most important model systems in vertebrate developmental biology. The development and function of its auditory brainstem circuitry is exceptionally well studied. These circuits represent an excellent system for genetic manipulation to investigate mechanisms controlling neural circuit formation, synaptogenesis, neuronal polarity, and dendritic arborization. The present study investigates the auditory nucleus, nucleus magnocellularis (NM). The neurotrophin receptor TrkB regulates dendritic structure in CNS neurons. TrkB is expressed in NM neurons at E7-E8 when these neurons have dendritic arbors. Downregulation of TrkB occurs after E8 followed by retraction of dendrites and by E18 most NM cells are adendritic. Is cessation of TrkB expression in NM necessary for dendritic retraction? To answer this question we combined focal in ovo electroporation with transposon mediated gene transfer to obtain stable expression of Doxycycline (Dox) regulated transgenes, specifically TrkB coexpressed with EGFP in a temporally controlled manner. Electroporation was performed at E2 and Dox added onto the chorioallointoic membrane from E7.5 to E16. Expression of EGFP had no effect on development of the embryo, or cell morphology and organization of auditory brainstem nuclei. NM cells expressing EGFP and TrkB at E17-E18 had dendrites and biophysical properties uncharacteristic for normal NM cells, indicating that cessation of TrkB expression is essential for dendrite retraction and functional maturation of these neurons. These studies indicate that expression of transposon based plasmids is an effective method to genetically manipulate events in mid to late embryonic brain development in chick.

Exploring Electrode Placements to Optimize the Identification and Measurement of Early Auditory Evoked Potentials.

Cochlear synaptic loss (termed cochlear synaptopathy) has been suggested to contribute to suprathreshold hearing difficulties. However, its existence and putative effects in humans remain inconclusive, largely due to the heterogeneous methods used across studies to indirectly evaluate the health of cochlear synapses. There is a need to standardize proxies of cochlear synaptopathy to appropriately compare and interpret findings across studies. Early auditory evoked potentials (AEPs), including the compound action potential (AP)/Wave I of the auditory brainstem response are a popular proxy, yet remain variable based on technical considerations. This study evaluated one such consideration-electrode array (i.e., montage)-to optimize the use of early AEP waveforms. In 35 young adults, electrocochleography (ECochG) responses were collected using vertical and horizontal montages. Standard ECochG measures and AP/Wave I and Wave II peak-to-trough amplitudes and latencies were compared between montages. Vertical montage recordings consistently produced significantly larger AP/Wave I peak-to-trough amplitudes compared to horizontal recordings. These findings support the use of a vertical electrode montage for optimal recordings of peripheral cochlear nerve activity. As cochlear synaptopathy continues to be explored in humans, the methods highlighted here should be considered in the development of a standardized assessment.

A Comprehensive Study on the Electrostatic Properties of Tubulin-Tubulin Complexes in Microtubules.

Microtubules are key players in several stages of the cell cycle and are also involved in the transportation of cellular organelles. Microtubules are polymerized by α/ß tubulin dimers with a highly dynamic feature, especially at the plus ends of the microtubules. Therefore, understanding the interactions among tubulins is crucial for characterizing microtubule dynamics. Studying microtubule dynamics can help researchers make advances in the treatment of neurodegenerative diseases and cancer. In this study, we utilize a series of computational approaches to study the electrostatic interactions at the binding interfaces of tubulin monomers. Our study revealed that among all the four types of tubulin-tubulin binding modes, the electrostatic attractive interactions in the α/ß tubulin binding are the strongest while the interactions of α/α tubulin binding in the longitudinal direction are the weakest. Our calculations explained that due to the electrostatic interactions, the tubulins always preferred to form α/ß tubulin dimers. The interactions between two protofilaments are the weakest. Thus, the protofilaments are easily separated from each other. Furthermore, the important residues involved in the salt bridges at the binding interfaces of the tubulins are identified, which illustrates the details of the interactions in the microtubule. This study elucidates some mechanistic details of microtubule dynamics and also identifies important residues at the binding interfaces as potential drug targets for the inhibition of cancer cells.

HIT-2: Implementing machine learning algorithms to treat bound ions in biomolecules.

Electrostatic features are fundamental to protein functions and protein-protein interactions. Studying highly charged biomolecules is challenging given the heterogeneous distribution of the ionic cloud around such biomolecules. Here we report a new computational method, Hybridizing Ions Treatment-2 (HIT-2), which is used to model biomolecule-bound ions using the implicit solvation model. By modeling ions, HIT-2 allows the user to calculate important electrostatic features of the biomolecules. HIT-2 applies an efficient algorithm to calculate the position of bound ions from molecular dynamics simulations. Modeling parameters were optimized by machine learning methods from thousands of datasets. The optimized parameters produced results with errors lower than 0.2 Å. The testing results on bound Ca2+ and Zn2+ in NAMD simulations also proved that HIT-2 can effectively identify bound ion types, numbers, and positions. Also, multiple tests performed on HIT-2 suggest the method can handle biomolecules that undergo remarkable conformational changes. HIT-2 can significantly improve electrostatic calculations for many problems in computational biophysics.

Phosphorylation of Tyrosine 841 Plays a Significant Role in JAK3 Activation.

Janus Kinase 3 (JAK3) plays a key role in the development, proliferation, and differentiation of various immune cells. It regulates gene expression by phosphorylation of Signal Transducers and Activators of Transcriptions (STATs) via the JAK/STAT pathway. Recently, we found a new JAK3 phosphorylation site, tyrosine 841 (Y841). The results showed that pY841 helps the kinase domain flip around the pseudo kinase domain, which may cause JAK3 conformational changes. It also reduces the size of the cleft between the N-lobe and the C-lobe of the JAK3 kinase domain. However, pY841 was found to enlarge the cleft when ATP/ADP was bound to the kinase. The increase in the cleft size suggested that pY841 enhanced the elasticity of the kinase domain. For unphosphorylated JAK3 (JAK3-Y841), the binding forces between the kinase domain and ATP or ADP were similar. After phosphorylation of Y841, JAK3-pY841 exhibited more salt bridges and hydrogen bonds between ATP and the kinase than between ADP and the kinase. Consequently, the electrostatic binding force between ATP and the kinase was higher than that between ADP and the kinase. The result was that compared to ADP, ATP was more attractive to JAK3 when Y841 was phosphorylated. Therefore, JAK3-pY841 tended to bind ATP rather than ADP. This work provides new insights into the role of phosphorylation in kinase activation and ATP hydrolysis and sheds light on the importance of understanding the molecular mechanisms that regulate the kinase function.