Identifying Key Binding Interactions Between the Cardiac L-Type Calcium Channel and Calmodulin Using Molecular Dynamics Simulations.

Defects in the binding of the calcium sensing protein calmodulin (CaM) to the L-type calcium channel (CaV1.2) or to the ryanodine receptor type 2 (RyR2) can lead to dangerous cardiac arrhythmias with distinct phenotypes, such as long-QT syndrome (LQTS) and catecholaminergic ventricular tachycardia (CPVT). Certain CaM mutations lead to LQTS while other mutations lead to CPVT, but the mechanisms by which a specific mutation can lead to each disease phenotype are not well-understood. In this study, we use long, 2 µs molecular dynamics simulations and a multitrajectory approach to identify the key binding interactions between the IQ domain of CaV1.2 and CaM. Five key interactions are found between CaV1.2 and CaM in the C-lobe, 1 in the central linker, and 2 in the N-lobe. In addition, while 5 key interactions appear between residues 120-149 in the C-lobe of CaM when it interacts with CaV1.2, only 1 key interaction is found within this region of CaM when it interacts with the RyR2. We show that this difference in the distribution of key interactions correlates with the known distribution of CaM mutations that lead to LQTS or CPVT. This correlation suggests that a disruption of key binding interactions is a plausible mechanism that can lead to these two different disease phenotypes.

Overcoming analytical and preanalytical challenges associated with extragenital home collected STI specimens.

Home sample collection for sexually transmitted infection (STI) screening options can improve access to sexual healthcare across communities. For Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), genital infections have classically been the focus for remote collection options. However, infections may go undiagnosed if sampling is limited to urogenital sites because some individuals only participate in oral and/or anal intercourse. Here we evaluated samples for CT/NG detection after several pre-analytical collection challenges. A paired provider to self-collection validation was performed on rectal [n = 162; 22 + for CT and 9 + for NG by provider-collected (PC)] and throat (N = 158; 2 + for CT and 11 + for NG by provider-collected) swabs. The positive percent agreement for CT and NG ranged from 90.9% to 100%. The discrepancies were more often positive on self-collected (SC) (n = 9 SC+/PC-; n = 1 PC+/SC-; n = 1 PC+/SC Equiv.; n = 2 PC-/SC Equiv.). An empirical limit of detection (LoD) lower than the manufacturer's claim (0.031 vs 2.5 IFU/mL for CT and 0.063 vs 124.8 CFU/ml for NG, respectively) was used to challenge additional variables. Common hand contaminants, including soap, hand sanitizer, lotion, and sunscreen were added to known positive (3× empirical LoD) or negative samples and did not influence detection. Samples at 2× and 10× the empirical LoD were challenged with extreme temperature cycling and extended room temperature storage. Detection was not affected by these conditions. These results indicate that remote self-collection is an appropriate method of sample acquisition for detecting extragenital CT/NG infections. Additionally, they provide a foundation towards meeting the regulatory standards for commercial testing of home collected extragenital samples. IMPORTANCE: There is a clinical need for expanded extragenital bacterial sexually transmitted infection (STI) testing options, but the current regulatory landscape limits the wide-spread promotion and adoption of such services. Improved access, particularly for the LGBTQ+ community, can be achieved by validating testing for specimens that are self-collected at a remote location and arrive at the laboratory via a postal carrier or other intermediary route. Here we provide valuable data showing that self-collected samples for anal and oropharyngeal STI testing are equally or increasingly sensitive compared with those collected by a provider. We systematically consider the effects of storage time, exposure to temperature extremes, and the addition of common toiletries on results.

A structure-based computational model of IP3R1 incorporating Ca and IP3 regulation.

The inositol 1,4,5-triphosphate receptor (IP3R) mediates Ca release in many cell types and is pivotal to a wide range of cellular processes. High-resolution cryoelectron microscopy studies have provided new structural details of IP3R type 1 (IP3R1), showing that channel function is determined by the movement of various domains within and between each of its four subunits. Channel properties are regulated by ligands, such as Ca and IP3, which bind at specific sites and control the interactions between these domains. However, it is not known how the various ligand-binding sites on IP3R1 interact to control the opening of the channel. In this study, we present a coarse-grained model of IP3R1 that accounts for the channel architecture and the location of specific Ca- and IP3-binding sites. This computational model accounts for the domain-domain interactions within and between the four subunits that form IP3R1, and it also describes how ligand binding regulates these interactions. Using a kinetic model, we explore how two Ca-binding sites on the cytosolic side of the channel interact with the IP3-binding site to regulate the channel open probability. Our primary finding is that the bell-shaped open probability of IP3R1 provides constraints on the relative strength of these regulatory binding sites. In particular, we argue that a specific Ca-binding site, whose function has not yet been established, is very likely a channel antagonist. Additionally, we apply our model to show that domain-domain interactions between neighboring subunits exert control over channel cooperativity and dictate the nonlinear response of the channel to Ca concentration. This suggests that specific domain-domain interactions play a pivotal role in maintaining the channel's stability, and a disruption of these interactions may underlie disease states associated with Ca dysregulation.

Trend analysis and prediction of seasonal changes in milk composition from a pasture-based dairy research herd.

The composition of seasonal pasture-produced milk is influenced by stage of lactation, animal genetics, and nutrition, which affects milk nutritional profile and processing characteristics. The objective was to study the effect of lactation stage (early, mid, and late lactation) and diet on milk composition in an Irish spring calving dairy research herd from 2012 to 2020 using principal component and predictive analytics. Crude protein, casein, fat, and solids increased from 2012 to 2020, whereas lactose concentration peaked in 2017, then decreased. Based on seasonal data from 2013 to 2016, forecasting models were successfully created to predict milk composition for 2017 to 2020. The diet of cows in this study is dependent upon grass growth rates across the milk production season, which in turn, are influenced by weather patterns, whereby extreme weather conditions (rainfall and temperature) were correlated with decreasing grass growth and increasing nonprotein nitrogen levels in milk. The study demonstrates a significant change in milk composition since 2012 and highlights the effect that seasonal changes such as weather and grass growth have on milk composition of pasture-based systems. The potential to forecast milk composition at different stages of lactation benefits processers by facilitating the optimization of in-process and supply logistics of dairy products.

The role of subunit cooperativity on ryanodine receptor 2 calcium signaling.

The ryanodine receptor type 2 (RyR2) is composed of four subunits that control calcium (Ca) release in cardiac cells. RyR2 serves primarily as a Ca sensor and can respond to rapid sub-millisecond pulses of Ca while remaining shut at resting concentrations. However, it is not known how the four subunits interact for the RyR2 to function as an effective Ca sensor. To address this question, and to understand the role of subunit cooperativity in Ca-mediated signal transduction, we have developed a computational model of the RyR2 composed of four interacting subunits. We first analyze the statistical properties of a single RyR2 tetramer, where each subunit can exist in a closed or open conformation. Our findings indicate that the number of subunits in the open state is a crucial parameter that dictates RyR2 kinetics. We find that three or four open subunits are required for the RyR2 to harness cooperative interactions to respond to sub-millisecond changes in Ca, while at the same time remaining shut at the resting Ca levels in the cardiac cell. If the required number of open subunits is lowered to one or two, the RyR2 cannot serve as a robust Ca sensor, as the large cooperativity required to stabilize the closed state prevents channel activation. Using this four-subunit model, we analyze the kinetics of Ca release from a RyR2 cluster. We show that the closure of a cluster of RyR2 channels is highly sensitive to the balance of cooperative interactions between closed and open subunits. Based on this result, we analyze how specific interactions between RyR2 subunits can induce persistent Ca leak from the sarcoplasmic reticulum (SR), which is believed to be arrhythmogenic. Thus, these results provide a framework to analyze how a pharmacologic or genetic modification of RyR2 subunit cooperativity can induce abnormal Ca cycling that can potentially lead to life-threatening arrhythmias.

Molecular Dynamics Simulations of the Cardiac Ryanodine Receptor Type 2 (RyR2) Gating Mechanism.

Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to fatal cardiac arrhythmias such as catecholaminergic polymorphic ventricular tachycardia (CPVT). While many CPVT mutations are associated with an increase in Ca2+ leak from the sarcoplasmic reticulum, the mechanistic details of RyR2 channel gating are not well understood, and this poses a barrier in the development of new pharmacological treatments. To address this, we explore the gating mechanism of the RyR2 using molecular dynamics (MD) simulations. We test the effect of changing the conformation of certain structural elements by constructing chimera RyR2 structures that are derived from the currently available closed and open cryo-electron microscopy (cryo-EM) structures, and we then use MD simulations to relax the system. Our key finding is that the position of the S4-S5 linker (S4S5L) on a single subunit can determine whether the channel as a whole is open or closed. Our analysis reveals that the position of the S4S5L is regulated by interactions with the U-motif on the same subunit and with the S6 helix on an adjacent subunit. We find that, in general, channel gating is crucially dependent on high percent occupancy interactions between adjacent subunits. We compare our interaction analysis to 49 CPVT1 mutations in the literature and find that 73% appear near a high percent occupancy interaction between adjacent subunits. This suggests that disruption of cooperative, high percent occupancy interactions between adjacent subunits is a primary cause of channel leak and CPVT in mutant RyR2 channels.

Voltage-mediated mechanism for calcium wave synchronization and arrhythmogenesis in atrial tissue.

A wide range of atrial arrythmias are caused by molecular defects in proteins that regulate calcium (Ca) cycling. In many cases, these defects promote the propagation of subcellular Ca waves in the cell, which can perturb the voltage time course and induce dangerous perturbations of the action potential (AP). However, subcellular Ca waves occur randomly in cells and, therefore, electrical coupling between cells substantially decreases their effect on the AP. In this study, we present evidence that Ca waves in atrial tissue can synchronize in-phase owing to an order-disorder phase transition. In particular, we show that, below a critical pacing rate, Ca waves are desynchronized and therefore do not induce substantial AP fluctuations in tissue. However, above this critical pacing rate, Ca waves gradually synchronize over millions of cells, which leads to a dramatic amplification of AP fluctuations. We exploit an underlying Ising symmetry of paced cardiac tissue to show that this transition exhibits universal properties common to a wide range of physical systems in nature. Finally, we show that in the heart, phase synchronization induces spatially out-of-phase AP duration alternans which drives wave break and reentry. These results suggest that cardiac tissue exhibits a phase transition that is required for subcellular Ca cycling defects to induce a life-threatening arrhythmia.

Computational Analysis of Binding Interactions between the Ryanodine Receptor Type 2 and Calmodulin.

Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to a variety of cardiac arrhythmias, such as catecholaminergic polymorphic ventricular tachycardia (CPVT). RyR2 is regulated by calmodulin (CaM), and mutations that disrupt their interaction can cause aberrant calcium release, leading to an arrhythmia. It was recently shown that increasing the RyR2-CaM binding affinity could rescue a defective CPVT-related RyR2 channel to near wild-type behavior. However, the interactions that determine the binding affinity at the RyR2-CaM binding interface are not well understood. In this study, we identify the key domains and interactions, including several new interactions, involved in the binding of CaM to RyR2. Also, our comparison between the wild-type and V3599K mutant suggests how the RyR2-CaM binding affinity can be increased via a change in the central and N-terminal lobe binding contacts for CaM. This computational approach provides new insights into the effect of a mutation at the RyR2-CaM binding interface, and it may find utility in drug design for the future treatment of cardiac arrhythmias.

Predictors and consequences of non-suicidal self-injury in relation to life, peer, and school factors.

INTRODUCTION: Numerous life, peer, and school-related factors have been found to be associated with non-suicidal self-injury (NSSI) among adolescents; however, most studies have not explored the possible reciprocal nature of these associations. The aim of the current study was to examine bidirectional and longitudinal associations between NSSI and several life, peer, and school-related factors (i.e., stressful life events, peer relationships, academic achievement, and attitudes towards school). METHOD: Community-based adolescents completed questionnaires assessing the variables of interest at three time points; age 12 (T1; 55.09% girls), age 13 (T2; 56.95% girls), and ages 14-15 (T3; 57.41% girls). In total, 529 adolescents provided complete data across all three-time points. RESULTS: Analyses showed a bidirectional association between NSSI and both attitudes towards school and stressful life events. Specifically, stressful life events at T2 predicted engagement in NSSI at T3, and NSSI at T2 predicted increased risk of stressful life events at T3. Similarly, having negative attitudes towards school predicted NSSI at T2, which, in turn, predicted negative attitudes towards school at T3. Further, academic achievement at T1 was negatively associated with NSSI at T2. Peer relationships were neither a predictor nor a consequence of NSSI. CONCLUSIONS: Our results suggest that NSSI can be both a predictor and a consequence of various life, and school factors. Focus on these factors in prevention and intervention efforts for NSSI among adolescents may be warranted.

Mechanistic link between CaM-RyR2 interactions and the genesis of cardiac arrhythmia.

In this study, we develop a computational model of the interaction between ryanodine receptor type 2 (RyR2) and calmodulin (CaM) to explore the mechanistic link between CaM-RyR2 interactions and cardiac arrhythmia. Our starting point is a biophysically based computational model of CaM binding to a single RyR2 subunit, which reproduces single-channel RyR2 measurements in lipid bilayers. We then integrate this CaM-RyR2 model into a spatially distributed whole-cell model of Ca cycling, which is used to investigate the relationship between CaM and Ca cycling homeostasis. We show that a reduction in CaM concentration leads to a substantial increase in the rate of spontaneous Ca sparks, and this induces a marked reduction in sarcoplasmic reticulum Ca load during steady-state pacing. Also, we show that a reduction in CaM modifies the RyR2 open probability, which makes the cell more prone to Ca wave propagation. These results indicate that aberrant Ca cycling activity during pacing is determined by the interplay between sarcoplasmic reticulum load reduction and the threshold for Ca wave propagation. Based on these results, we show that when CaM is reduced, Ca waves can occur in a cell and induce action potential perturbations that are arrhythmogenic. Thus, this study outlines a novel, to our knowledge, mechanistic link between CaM-RyR2 binding kinetics and the induction of arrhythmias in the heart.

Correction: Brain structure in pediatric Tourette syndrome.

In this published article, members of 'The Tourette Association of America Neuroimaging Consortium' were not cited in PubMed. These consortium members are listed in the associated correction.

Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.

Membrane-bound protein receptors are a primary biological drug target, but the computational analysis of membrane proteins has been limited. In order to improve molecular mechanics Poisson-Boltzmann surface area (MMPBSA) binding free energy calculations for membrane protein-ligand systems, we have optimized a new heterogeneous dielectric implicit membrane model, with respect to free energy simulations in explicit membrane and explicit water, and implemented it into the Amber software suite. This new model supersedes our previous uniform, single dielectric implicit membrane model by allowing the dielectric constant to vary with depth within the membrane. We calculated MMPBSA binding free energies for the human purinergic platelet receptor (P2Y12R) and two of the muscarinic acetylcholine receptors (M2R and M3R) bound to various antagonist ligands using both membrane models, and we found that the heterogeneous dielectric membrane model has a stronger correlation with experimental binding affinities compared to the older model under otherwise identical conditions. This improved membrane model increases the utility of MMPBSA calculations for the rational design and improvement of future drug candidates.

A proposal for an atypical femur fracture treatment and prevention clinical practice guideline.

The prevention as well as the treatment of atypical femur fractures (AFFs) remains controversial but there have been many clinical recommendations suggested. We have summarized these recommendations as well as expanded upon them in this paper. INTRODUCTION: The purpose of the paper was to develop a clinical practice guideline that both treats AFF and decreases the risk of AFF in patients requiring antiresorptive medications. Examples of these medications include bisphosphonates and denosumab for the treatment of osteoporosis. METHODS: A literature review looking for recommendations on AFF identification, management, and prevention was done. We also performed an updated review of clinical guidelines on AFF prevention and treatment that were developed for the Kaiser Permanente osteoporosis/fracture prevention team. RESULTS: Concise clinical practice guidelines are presented that can be applied in treatment of AFF as well as help reduce the risk of developing an AFF in patients requiring antiresorptive medications. These guidelines are based on using both typical fracture and AFF risk assessment to determine duration of antiresorptive of 3 to 5 years before consideration if a drug holiday is needed. Specific groups such as younger Asian women should be reassessed at 3 years with DXA and FRAX to see if a drug holiday is needed whereas patients at higher risk for typical fractures may be reassessed at 5 years of treatment. The DXA rescreening can now be accessed if focal or generalized lateral cortex changes are present that may indicate incomplete AFFs are present. If an incomplete AFF is discovered either by DXA or by other imaging studies, it is imperative to stop antiresorptive medications and to take additional measures to lower the risk of progression to a complete AFF. If complete AFF does occur, then antiresorptive medications should be stopped and additional measures should be taken to decrease the risk of developing an AFF on the contralateral femur. CONCLUSIONS: Clinical practice guidelines for the treatment and prevention of AFF will benefit clinicians who are frequently faced with having to make clinical decisions in patients requiring antiresorptive medications.

Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aß) Antibodies.

Alzheimer's disease (AD) is a neurodegenerative disorder that lacks effective treatment options. Anti-amyloid beta (Aß) antibodies are the leading drug candidates to treat AD, but the results of clinical trials have been disappointing. Introducing rational mutations into anti-Aß antibodies to increase their effectiveness is a way forward, but the path to take is unclear. In this study, we demonstrate the use of computational fragment-based docking and MMPBSA binding free energy calculations in the analysis of anti-Aß antibodies for rational drug design efforts. Our fragment-based docking method successfully predicts the emergence of the common EFRH epitope. MD simulations coupled with MMPBSA binding free energy calculations are used to analyze scenarios described in prior studies, and we computationally introduce rational mutations into PFA1 to predict mutations that can improve its binding affinity toward the pE3-Aß3-8 form of Aß. Two out of our four proposed mutations are predicted to stabilize binding. Our study demonstrates that a computational approach may lead to an improved drug candidate for AD in the future.

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. Computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here, we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: (1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. (2) The highly different accessibilities in the membrane and water regions are addressed with a two-step, two-probe grid-labeling procedure. (3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 Å for globular proteins is a very reasonable default value for membrane protein simulations. It gives the best compromise in reproducing the explicit water distributions in membrane channel proteins, at least in the water accessible pore/channel regions. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe good agreement with the experimental results.

Recent Developments and Applications of the MMPBSA Method.

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.

Brain structure in pediatric Tourette syndrome.

Previous studies of brain structure in Tourette syndrome (TS) have produced mixed results, and most had modest sample sizes. In the present multicenter study, we used structural magnetic resonance imaging (MRI) to compare 103 children and adolescents with TS to a well-matched group of 103 children without tics. We applied voxel-based morphometry methods to test gray matter (GM) and white matter (WM) volume differences between diagnostic groups, accounting for MRI scanner and sequence, age, sex and total GM+WM volume. The TS group demonstrated lower WM volume bilaterally in orbital and medial prefrontal cortex, and greater GM volume in posterior thalamus, hypothalamus and midbrain. These results demonstrate evidence for abnormal brain structure in children and youth with TS, consistent with and extending previous findings, and they point to new target regions and avenues of study in TS. For example, as orbital cortex is reciprocally connected with hypothalamus, structural abnormalities in these regions may relate to abnormal decision making, reinforcement learning or somatic processing in TS.

Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor.

Membrane proteins, due to their roles as cell receptors and signaling mediators, make prime candidates for drug targets. The computational analysis of protein-ligand binding affinities has been widely employed as a tool in rational drug design efforts. Although efficient implicit solvent-based methods for modeling globular protein-ligand binding have been around for many years, the extension of such methods to membrane protein-ligand binding is still in its infancy. In this study, we extended the widely used Amber/MMPBSA method to model membrane protein-ligand systems, and we used it to analyze protein-ligand binding for the human purinergic platelet receptor (P2Y12R), a prominent drug target in the inhibition of platelet aggregation for the prevention of myocardial infarction and stroke. The binding affinities, computed by the Amber/MMPBSA method using standard parameters, correlate well with experiment. A detailed investigation of these parameters was conducted to assess their impact on the accuracy of the method. These analyses show the importance of properly treating the nonpolar solvation interactions and the electrostatic polarization in the binding of nucleotide agonists and non-nucleotide antagonists to P2Y12R. On the basis of the crystal structures and the experimental conditions in the binding assay, we further hypothesized that the nucleotide agonists lose their bound magnesium ion upon binding to P2Y12R, and our computational study supports this hypothesis. Ultimately, this work illustrates the value of computational analysis in the interpretation of experimental binding reactions.

Approximate analytical solutions for excitation and propagation in cardiac tissue.

It is well known that a variety of cardiac arrhythmias are initiated by a focal excitation in heart tissue. At the single cell level these currents are typically induced by intracellular processes such as spontaneous calcium release (SCR). However, it is not understood how the size and morphology of these focal excitations are related to the electrophysiological properties of cardiac cells. In this paper a detailed physiologically based ionic model is analyzed by projecting the excitation dynamics to a reduced one-dimensional parameter space. Based on this analysis we show that the inward current required for an excitation to occur is largely dictated by the voltage dependence of the inward rectifier potassium current (I(K1)), and is insensitive to the detailed properties of the sodium current. We derive an analytical expression relating the size of a stimulus and the critical current required to induce a propagating action potential (AP), and argue that this relationship determines the necessary number of cells that must undergo SCR in order to induce ectopic activity in cardiac tissue. Finally, we show that, once a focal excitation begins to propagate, its propagation characteristics, such as the conduction velocity and the critical radius for propagation, are largely determined by the sodium and gap junction currents with a substantially lesser effect due to repolarizing potassium currents. These results reveal the relationship between ion channel properties and important tissue scale processes such as excitation and propagation.