Allosterism in the PDZ Family.

Dynamic allosterism allows the propagation of signal throughout a protein. The PDZ (PSD-95/Dlg1/ZO-1) family has been named as a classic example of dynamic allostery in small modular domains. While the PDZ family consists of more than 200 domains, previous efforts have primarily focused on a few well-studied PDZ domains, including PTP-BL PDZ2, PSD-95 PDZ3, and Par6 PDZ. Taken together, experimental and computational studies have identified regions of these domains that are dynamically coupled to ligand binding. These regions include the αA helix, the αB lower-loop, and the αC helix. In this review, we summarize the specific residues on the αA helix, the αB lower-loop, and the αC helix of PTP-BL PDZ2, PSD-95 PDZ3, and Par6 PDZ that have been identified as participants in dynamic allostery by either experimental or computational approaches. This review can serve as an index for researchers to look back on the previously identified allostery in the PDZ family. Interestingly, our summary of previous work reveals clear consistencies between the domains. While the PDZ family has a low sequence identity, we show that some of the most consistently identified allosteric residues within PTP-BL PDZ2 and PSD-95 PDZ3 domains are evolutionarily conserved. These residues include A46/A347, V61/V362, and L66/L367 on PTP-BL PDZ2 and PSD-95 PDZ3, respectively. Finally, we expose a need for future work to explore dynamic allostery within (1) PDZ domains with multiple binding partners and (2) multidomain constructs containing a PDZ domain.

Spectroscopic and Dynamic Properties of Electronically Excited Pendant Porphyrin Polymers with Backbones of Differing Flexibility.

A zinc porphyrin-pendant norbornene polymer with a rigid backbone characterized by a 2:1 E/Z isomeric structure ratio has been synthesized, and its spectroscopic and photophysical properties are examined. Zinc tetraphenylporphyrin, the porphyrin-substituted norbornene monomer, and a previously reported zinc porphyrin-pendant polymer with a flexible polymethylene backbone have been used as comparators. Unlike its flexible counterpart, the rigid norbornene polymer exhibits clear exciton splitting of its Soret band, much more rapid relaxation rates of its excited singlet states, and a very small yield of an unusually short-lived triplet state. Unlike the flexible pendant polymer, which exhibits excimeric S2 fluorescence as a result of chromophore rotation, anti-Kasha emission from the norbornene polymer originates primarily from the unperturbed porphyrin E region. The low triplet yield in the polymer is attributed to greatly increased rates of competing internal conversion within the singlet manifold. Nevertheless, upconverted delayed fluorescence that is quenched by oxygen is observed upon intense steady-state Q-band excitation of degassed polymer solutions, signaling direct triplet involvement. Consistent with the polymer's rigid structure, this biexcitonic process is assigned to ultrafast singlet exciton migration and triplet-triplet annihilation following absorption of a second photon by the small steady-state concentration of polymer triplets.

Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer.

During the first steps of photosynthesis, the energy of impinging solar photons is transformed into electronic excitation energy of the light-harvesting biomolecular complexes. The subsequent energy transfer to the reaction center is commonly rationalized in terms of excitons moving on a grid of biomolecular chromophores on typical timescales [Formula: see text]100 fs. Today's understanding of the energy transfer includes the fact that the excitons are delocalized over a few neighboring sites, but the role of quantum coherence is considered as irrelevant for the transfer dynamics because it typically decays within a few tens of femtoseconds. This orthodox picture of incoherent energy transfer between clusters of a few pigments sharing delocalized excitons has been challenged by ultrafast optical spectroscopy experiments with the Fenna-Matthews-Olson protein, in which interference oscillatory signals up to 1.5 ps were reported and interpreted as direct evidence of exceptionally long-lived electronic quantum coherence. Here, we show that the optical 2D photon echo spectra of this complex at ambient temperature in aqueous solution do not provide evidence of any long-lived electronic quantum coherence, but confirm the orthodox view of rapidly decaying electronic quantum coherence on a timescale of 60 fs. Our results can be considered as generic and give no hint that electronic quantum coherence plays any biofunctional role in real photoactive biomolecular complexes. Because in this structurally well-defined protein the distances between bacteriochlorophylls are comparable to those of other light-harvesting complexes, we anticipate that this finding is general and directly applies to even larger photoactive biomolecular complexes.

Executive Control in Early Childhood as an Antecedent of Adolescent Problem Behaviors: A Longitudinal Study with Performance-based Measures of Early Childhood Cognitive Processes.

Identifying childhood cognitive processes that predict adolescent problem behaviors can help guide understanding and prevention of these behaviors. In a community sample of 313 youth recruited in a small Midwestern city between 2006 and 2012 (49% male, 64% European American), executive control and foundational cognitive abilities were assessed at age 5 in a lab setting with performance-based measures. In adolescence, youth provided self-report of problem behaviors in surveys administered annually between ages 14 and 16. Executive control was negatively associated with externalizing behavior problems and adolescents getting in trouble at school, accounting for foundational cognitive abilities and family background covariates. Executive control had negative, but nonsignificant, associations with internalizing problems and substance use initiation. The findings point to deficits in executive control as a childhood risk factor for later problems and a potential target for preventive interventions.

Immiscible Anionic Gemini Surfactant-Perfluorinated Fatty Acid Langmuir Monolayer Films.

A new member of the N,N,N',N'-dialkyl-N,N'-diacetate ethylenediamine family of anionic gemini surfactants has been synthesized, and its miscibility with the model perfluorocarbon, perfluorotetradecanoic acid (PF), has been investigated in monolayer films at the air-water interface. Thermodynamics of mixing and the accompanying changes in the mixed film structure have been probed using a combination of compression isotherm measurements supported by Brewster angle microscope imaging and X-ray scattering measurements, and results have been compared with those collected for a previously studied, shorter tail chain variant of the surfactant. Thermodynamic measurements showed that the gemini surfactant and perfluorotetradecanoic acid were immiscible, with weak repulsive interactions, manifesting as small positive deviations from ideal mixing, observed between the two film components. Films were highly textured, with micrometer-scale, phase-separated domains readily detectable. Grazing incidence X-ray diffraction measurements showed that the gemini surfactant was disordered in the monolayers, whereas the perfluorocarbon formed discrete crystallites in the disordered matrix. Despite the small deviations from ideal mixing detected in the thermodynamic measurements, the X-ray measurements indicated that the presence of the gemini perturbs the PF crystal lattice from that of pure PF. Finally, X-ray reflectivity measurements showed that the addition of equimolar PF to the gemini monolayer induces a significant increase in the nominal head group thickness of the film, suggesting that interactions between the two surfactants can lead to structural rearrangements of gemini's head group near to the water surface.

Exciton Dynamics of Photoexcited Pendant Porphyrin Polymers in Solution and in Thin Films.

Several new polymers with rotatable zinc porphyrin pendants have been synthesized and their optical spectroscopic and photophysical properties, including upconversion efficiencies, determined in both fluid solution and thin films. Comparisons made with the ß-substituted zinc tetraphenylporphyrin monomers and ZnTPP itself reveal that the yield of triplets resulting from either Q-band or Soret-band excitation of the polymers is surprisingly small. A detailed kinetic analysis of the fluorescence decays and transient triplet absorptions of the substituted monomers and their corresponding polymers reveals that this phenomenon is due to two parallel internal singlet quenching processes assigned to transient intrachain excimer formation. Consequently, the yields of upconverted S2 fluorescence resulting from Q-band excitation in the degassed polymers are significantly diminished in both fluid solution and thin films. Implications of these results for the design of polymer upconverting systems are discussed.

Mixing Behavior in Binary Anionic Gemini Surfactant-Perfluorinated Fatty Acid Langmuir Monolayers.

The miscibility and film structure of mixed Langmuir monolayer films composed of an anionic gemini N,N,N',N'-dialkyl-N,N'-diacetate ethylenediamine surfactant (Ace(12)-2-Ace(12)) with perfluorotetradecanoic acid (C13F27COOH; PF) have been investigated using a variety of thermodynamic and structural characterization methods. The two film components were found to be miscible in monolayers at the air-water interface over a range of compositions and at all but the lowest surface pressures, with attractive interactions occurring between the two components. While pure PF monolayers formed crystalline lattices with hexagonal symmetry and with the surfactant tails oriented normal to the underlying water subphase, the pure gemini surfactant formed amorphous films with little tendency to orient at the subphase. In mixed films with mole ratios of PF:Ace(12)-2-Ace(12) < 2.5, the miscibility of the two components resulted in a nearly complete loss of crystallinity of the PF, though films at higher mole fractions of PF showed some residual crystallinity, albeit with lattice structures that were significantly different from that of pure PF. Miscibility and film structure in this mixed system are discussed in comparison with other mixed gemini surfactant systems in the literature as well as binary mixtures of phospholipids or monomeric fatty acids with PF.

Psychometrics of the Symptoms and Functioning Severity Scale for High-Risk Youth.

Youth in residential care have significant mental health needs which require regular progress monitoring; however, very few emotional or behavioral assessments have been examined with this unique, high-risk population. This study examined the psychometrics of the Symptom Functioning and Severity Scale, a brief 24-item measure designed to assess the emotional and behavioral status of youth. This study examined the SFSS ratings from 143 youth with a disruptive behavior diagnosis living in a group-home facility in the Midwest and 52 of their service providers. Overall, the findings suggest that the psychometrics of the SFSS, when rated by staff or youth were similar to the original outpatient clinical samples. More specifically, the Rasch analyses indicate that the SFSS items and the overall scale is performing adequately, and the confirmatory factor analyses replicated the two-factor structure for staff. However, the fit of the two-factor model was less compelling for youth ratings. In all, the brief SFSS seems a promising measure for assessing problem severity for youth in residential care.

Examining Change in Therapeutic Alliance to Predict Youth Mental Health Outcomes.

OBJECTIVE: To examine the link between therapeutic alliance and youth outcomes. METHOD: The study was conducted at a group-home with 112 youth with a disruptive-behavior diagnosis. Therapeutic alliance was collected routinely via youth and staff report. Outcome data were collected using youth and staff reports of externalizing behavior as well as behavioral incidents occurring during care. Outcome data were collected following intake into services and at 6 and 12 months of care. Data were analyzed to examine (1) if youth behavior problems at intake were predictive of therapeutic alliance and (2) if changes in alliance were predictive of subsequent youth outcomes. These were conducted with a 6-month service-delivery model and replicated with a 12-month model. RESULTS: There was some support for the first hypothesis, that initial levels of youth externalizing behavior would be related to alliance ratings; however, most of the effects were marginally significant. The second hypothesis, that changes in therapeutic alliance would be related to subsequent youth outcomes, was supported for the 6-month model, but not the 12-month model. CONCLUSIONS: Changes in therapeutic alliance may be predictive of youth outcomes during care. Additional research into examining therapeutic alliance trajectories is warranted to improve mental health services for youth.

Validation of the symptoms and functioning severity scale in residential group care.

Tests that measure the emotional and behavioral problems of children and youth are typically not normed and standardized on youth diagnosed with disruptive behavior, particularly those youth in residential care. Yet professional standards mandate that before instruments are used with a specific population the psychometric properties need to be studied and re-established: specifically, psychometric properties, including validity, need to be evaluated (AERA, APA, and NCME, The standards for educational and psychological testing. AERA, Washington, DC, 1999). The purpose of the present study was to assess the validity characteristics of the Symptoms and Functioning Severity Scale (SFSS; Bickman et al., Manual of the Peabody Treatment Progress Battery, Vanderbilt University, Nashville, TN, 2010), a widely used test developed for use in outpatient clinics, with youth in a residential care program. The convergent validity of the SFSS was established with the large correlations (0.78-0.86) with the CBCL. Several binary classification analyses including specificity, area under the receiver operating characteristic curve, positive and negative likelihood ratios, and the Youden Index supported the validity of the SFSS. However, the sensitivity index was somewhat low indicating the test may produce a high level of false negatives. Limitations, future research and implications are discussed.

Associations between health and sexual lifestyles in Britain: findings from the third National Survey of Sexual Attitudes and Lifestyles (Natsal-3).

BACKGROUND: Physical and mental health could greatly affect sexual activity and fulfilment, but the nature of associations at a population level is poorly understood. We used data from the third National Survey of Sexual Attitudes and Lifestyles (Natsal-3) to explore associations between health and sexual lifestyles in Britain (England, Scotland, and Wales). METHODS: Men and women aged 16-74 years who were resident in households in Britain were interviewed between Sept 6, 2010, and Aug 31, 2012. Participants completed the survey in their own homes through computer-assisted face-to-face interviews and self-interview. We analysed data for self-reported health status, chronic conditions, and sexual lifestyles, weighted to account for unequal selection probabilities and non-response to correct for differences in sex, age group, and region according to 2011 Census figures. FINDINGS: Interviews were done with 15,162 participants (6293 men, 8869 women). The proportion reporting recent sexual activity (one or more occasion of vaginal, oral, or anal sex with a partner of the opposite sex, or oral or anal sex or genital contact with a partner of the same sex in the past 4 weeks) decreased with age after the age of 45 years in men and after the age of 35 years in women, while the proportion in poorer health categories increased with age. Recent sexual activity was less common in participants reporting bad or very bad health than in those reporting very good health (men: 35·7% [95% CI 28·6-43·5] vs 74·8% [72·7-76·7]; women: 34·0% [28·6-39·9] vs 67·4% [65·4-69·3]), and this association remained after adjusting for age and relationship status (men: adjusted odds ratio [AOR] 0·29 [95% CI 0·19-0·44]; women: 0·43 [0·31-0·61]). Sexual satisfaction generally decreased with age, and was significantly lower in those reporting bad or very bad health than in those reporting very good health (men: 45·4% [38·4-52·7] vs 69·5% [67·3-71·6], AOR 0·51 [0·36-0·72]; women: 48·6% [42·9-54·3] vs 65·6% [63·6-67·4], AOR 0·69 [0·53-0·91]). In both sexes, reduced sexual activity and reduced satisfaction were associated with limiting disability and depressive symptoms, and reduced sexual activity was associated with chronic airways disease and difficulty walking up the stairs because of a health problem. 16·6% (95% CI 15·4-17·7) of men and 17·2% (16·3-18·2) of women reported that their health had affected their sex life in the past year, increasing to about 60% in those reporting bad or very bad health. 23·5% (20·3-26·9) of men and 18·4% (16·0-20·9) of women who reported that their health affected their sex life reported that they had sought clinical help (>80% from general practitioners; <10% from specialist services). INTERPRETATION: Poor health is independently associated with decreased sexual activity and satisfaction at all ages in Britain. Many people in poor health report an effect on their sex life, but few seek clinical help. Sexual lifestyle advice should be a component of holistic health care for patients with chronic ill health. FUNDING: Grants from the UK Medical Research Council and the Wellcome Trust, with support from the Economic and Social Research Council and Department of Health.

Relational community engagement within health interventions at varied outcome scales.

Relational community engagement may be a powerful approach with multiple health outcomes. Relational community engagement has the potential to promote health and involves collaborative efforts between multiple stakeholders. The COVID-19 pandemic further highlighted the centrality of community engagement in health crises. Challenges continue to persist, however, in genuinely engaging and empowering communities for better health outcomes. Understanding the multi-level and complex relational nature of community engagement is essential to comprehend its influence on health at micro, meso, and macro scales of influence. The purpose of this narrative review was to synthesize the literature on relational community engagement within varied health interventions at the three major system levels (micro, meso, and macro) to support the development of future research agendas. At the micro level, relational community engagement interventions demonstrated a range of positive outcomes including: increased sense of control, satisfaction, positive behavior, improved knowledge, behavior change, empowerment, and overall positive health and social outcomes. At the meso level, relational community engagement interventions resulted in increased trust between stakeholders and groups/teams, and increased community senses of ownership of interventions, decisions, structures. At the macro level, relational community engagement interventions influenced broader societal factors and had positive impacts on health policy and governance including collaboration between sectors and communities as well as increased access to services. The review highlights the potential versatility and effectiveness of interventions that prioritize relationships, health promotion, and social change while underscoring the significance of holistic and community-centered approaches in addressing diverse health and social challenges.

Therapeutic Alliance Between Youth and Staff in Residential Group Care: Psychometrics of the Therapeutic Alliance Quality Scale.

Therapeutic alliance has been frequently studied in individual counseling sessions; however, research on therapeutic alliance in residential settings for youth with mental health diagnoses has been limited. This may be due, in part, to the presence of multiple service providers often in caregiving roles. The purpose of this study was to examine the psychometric quality of a widely utilized measure of therapeutic alliance used in psychotherapy with youth in residential care where the treatment is provided by a trained married couple. We also compared the relationship between youth ratings of their male and female service provider, as well as examined correlations in ratings between youth and staff on therapeutic alliance. Finally, we investigated the direction, magnitude, and trajectory of change in therapeutic alliance over a 12-month period following admission into residential care. The method was a longitudinal assessment of 135 youth and 124 staff regarding therapeutic alliance over the course of 12 months or discharge from services. Results indicated strong psychometric properties and high correlations for youth ratings of both their male and female service providers. However, the correlation was low between youth and service provider ratings of alliance. Longitudinal analyses indicated that rates of therapeutic alliance changed over time.

Investigating the Mechanical Properties and Flexibility of N-BAR Domains in PICK1 by Molecular Dynamics Simulations.

INTRODUCTION: The proteins of the Bin/Amphiphysin/Rvs167 (BAR) domain superfamily are believed to induce membrane curvature. PICK1 is a distinctive protein that consists of both a BAR and a PDZ domain, and it has been associated with numerous diseases. It is known to facilitate membrane curvature during receptor-mediated endocytosis. In addition to understanding how the BAR domain facilitates membrane curvature, it's particularly interesting to unravel the hidden links between the structural and mechanical properties of the PICK1 BAR domain. METHODS: This paper employs steered molecular dynamics (SMD) to investigate the mechanical properties associated with structural changes in the PICK1 BAR domains. RESULTS: Our findings suggest that not only do helix kinks assist in generating curvature of BAR domains, but they may also provide the additional flexibility required to initiate the binding between BAR domains and the membrane. CONCLUSION: We have observed a complex interaction network within the BAR monomer and at the binding interface of the two BAR monomers. This network is crucial for maintaining the mechanical properties of the BAR dimer. Owing to this interaction network, the PICK1 BAR dimer exhibits different responses to external forces applied in opposite directions.

Key Factors Regulating the Interdomain Dynamics May Contribute to the Assembly of ASC.

The canonical ASC domains, PYD and CARD, are interconnected by a lengthy, semi-flexible linker. The molecular basis and purpose of ASC's highly dynamic feature remain elusive. In this study, all-atom molecular dynamics simulations were utilized to examine the role of the linker and the interdomain dynamics of the ASC monomer. As revealed in the principal component analysis (PCA), the flexible linker enables interdomain dynamics and rotation. The stumbling between domains is partially attributed to the helical portion of N-terminal residues in the linker. Additionally, the linker exhibits a certain structural preference due to the turn-type structural inclination of the N-terminal and the presence of several prolines on the linker. Such structural preferences lead to the unavailability of regions for PYD type I interactions to CARDs, as evidenced by the CARD spatial restraint analysis. In conclusion, the semi-flexible linker introduces functionally relevant interdomain dynamics, potentially enhancing PYD self-assembly and the subsequent assembly of the inflammasome complex.

Emulsion-induced polymersomes taming tetrodotoxin for prolonged duration local anesthesia.

Injectable local anesthetics that can provide a continuous nerve block approximating the duration of a pain state would be a life-changing solution for patients experiencing post-operative pain or chronic pain. Tetrodotoxin (TTX) is a site 1 sodium channel blocker that is extremely potent compared to clinically used local anesthetics. Challengingly, TTX doses are limited by its associated systemic toxicity, thus shortening the achievable duration of nerve blocks. Here, we explore emulsion-induced polymersomes (EIP) as a drug delivery system to safely use TTX for local anesthesia. By emulsifying hyperbranched polyglycerol-poly (propylene glycol)-hyperbranched polyglycerol (HPG-PPG-HPG) in TTX aqueous solution, HPG-PPG-HPG self-assembled into micrometer-sized polymersomes within seconds. The formed polymersomes have microscopically visible internal aqueous pockets that encapsulate TTX with an encapsulation efficiency of up to 94%. Moreover, the polymersomes are structurally stable, enabling sustained TTX release. In vivo, the freshly prepared EIP/TTX formulation can be directly injected and increased the tolerated dose of TTX in Sprague-Dawley rats to 11.5 µg without causing any TTX-related systemic toxicity. In the presence of the chemical penetration enhancer (CPE) sodium octyl sulfate (SOS), a single perineural injection of EIP/TTX/SOS formulation produced a reliable sciatic nerve block for 22 days with minimal local toxicity.

Identification of ML204, a novel potent antagonist that selectively modulates native TRPC4/C5 ion channels.

Transient receptor potential canonical (TRPC) channels are Ca(2+)-permeable nonselective cation channels implicated in diverse physiological functions, including smooth muscle contractility and synaptic transmission. However, lack of potent selective pharmacological inhibitors for TRPC channels has limited delineation of the roles of these channels in physiological systems. Here we report the identification and characterization of ML204 as a novel, potent, and selective TRPC4 channel inhibitor. A high throughput fluorescent screen of 305,000 compounds of the Molecular Libraries Small Molecule Repository was performed for inhibitors that blocked intracellular Ca(2+) rise in response to stimulation of mouse TRPC4ß by µ-opioid receptors. ML204 inhibited TRPC4ß-mediated intracellular Ca(2+) rise with an IC(50) value of 0.96 µm and exhibited 19-fold selectivity against muscarinic receptor-coupled TRPC6 channel activation. In whole-cell patch clamp recordings, ML204 blocked TRPC4ß currents activated through either µ-opioid receptor stimulation or intracellular dialysis of guanosine 5'-3-O-(thio)triphosphate (GTPγS), suggesting a direct interaction of ML204 with TRPC4 channels rather than any interference with the signal transduction pathways. Selectivity studies showed no appreciable block by 10-20 µm ML204 of TRPV1, TRPV3, TRPA1, and TRPM8, as well as KCNQ2 and native voltage-gated sodium, potassium, and calcium channels in mouse dorsal root ganglion neurons. In isolated guinea pig ileal myocytes, ML204 blocked muscarinic cation currents activated by bath application of carbachol or intracellular infusion of GTPγS, demonstrating its effectiveness on native TRPC4 currents. Therefore, ML204 represents an excellent novel tool for investigation of TRPC4 channel function and may facilitate the development of therapeutics targeted to TRPC4.

Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction.

The inhibition of protein-protein interactions is a growing strategy in drug development. In addition to structured regions, many protein loop regions are involved in protein-protein interactions and thus have been identified as potential drug targets. To effectively target such regions, protein structure is critical. Loop structure prediction is a challenging subgroup in the field of protein structure prediction because of the reduced level of conservation in protein sequences compared to the secondary structure elements. AlphaFold 2 has been suggested to be one of the greatest achievements in the field of protein structure prediction. The AlphaFold 2 predicted protein structures near the X-ray resolution in the Critical Assessment of protein Structure Prediction (CASP 14) competition in 2020. The purpose of this work is to survey the performance of AlphaFold 2 in specifically predicting protein loop regions. We have constructed an independent dataset of 31,650 loop regions from 2613 proteins (deposited after the AlphaFold 2 was trained) with both experimentally determined structures and AlphaFold 2 predicted structures. With extensive evaluation using our dataset, the results indicate that AlphaFold 2 is a good predictor of the structure of loop regions, especially for short loop regions. Loops less than 10 residues in length have an average Root Mean Square Deviation (RMSD) of 0.33 Å and an average the Template Modeling score (TM-score) of 0.82. However, we see that as the number of residues in a given loop increases, the accuracy of AlphaFold 2's prediction decreases. Loops more than 20 residues in length have an average RMSD of 2.04 Å and an average TM-score of 0.55. Such a correlation between accuracy and length of the loop is directly linked to the increase in flexibility. Moreover, AlphaFold 2 does slightly over-predict α-helices and ß-strands in proteins.

Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain.

The PDZ family has drawn attention as possible drug targets because of the domains' wide ranges of function and highly conserved binding pockets. The PICK1 PDZ domain has been proposed as a possible drug target because the interactions between the PICK1 PDZ domain and the GluA2 subunit of the AMPA receptor have been shown to progress neurodegenerative diseases. BIO124 has been identified as a sub µM inhibitor of the PICK1-GluA2 interaction. Here, we use all-atom molecular dynamics simulations to reveal the atomic-level interaction pattern between the PICK1 PDZ domain and BIO124. Our simulations reveal three unique binding conformations of BIO124 in the PICK1 PDZ binding pocket, referred to here as state 0, state 1, and state 2. Each conformation is defined by a unique hydrogen bonding network and a unique pattern of hydrophobic interactions between BIO124 and the PICK1 PDZ domain. Interestingly, each conformation of BIO124 results in different dynamic changes to the PICK1 PDZ domain. Unlike states 1 and 2, state 0 induces dynamic coupling between BIO124 and the αA helix. Notably, this dynamic coupling with the αA helix is similar to what has been observed in other PDZ-ligand complexes. Our analysis indicates that the interactions formed between BIO124 and I35 may be the key to inducing dynamic coupling with the αA helix. Lastly, we suspect that the conformational shifts observed in our simulations may affect the stability and thus the overall effectiveness of BIO124. We propose that a physically larger inhibitor may be necessary to ensure sufficient interactions that permit stable binding between a drug and the PICK1 PDZ domain.

Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations.

The PDZ family is comprised of small modular domains that play critical roles in the allosteric modulation of many cellular signaling processes by binding to the C-terminal tail of different proteins. As dominant modular proteins that interact with a diverse set of peptides, it is of particular interest to explore how different binding partners induce different allosteric effects on the same PDZ domain. Because the PICK1 PDZ domain can bind different types of ligands, it is an ideal test case to answer this question and explore the network of interactions that give rise to dynamic allostery. Here, we use all-atom molecular dynamics simulations to explore dynamic allostery in the PICK1 PDZ domain by modeling two PICK1 PDZ systems: PICK1 PDZ-DAT and PICK1 PDZ-GluR2. Our results suggest that ligand binding to the PICK1 PDZ domain induces dynamic allostery at the αA helix that is similar to what has been observed in other PDZ domains. We found that the PICK1 PDZ-ligand distance is directly correlated with both dynamic changes of the αA helix and the distance between the αA helix and ßB strand. Furthermore, our work identifies a hydrophobic core between DAT/GluR2 and I35 as a key interaction in inducing such dynamic allostery. Finally, the unique interaction patterns between different binding partners and the PICK1 PDZ domain can induce unique dynamic changes to the PICK1 PDZ domain. We suspect that unique allosteric coupling patterns with different ligands may play a critical role in how PICK1 performs its biological functions in various signaling networks.