Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita-Baylis-Hillman Reaction: Why Is Enzyme Design so Difficult?

It is hoped that artificial enzymes designed in laboratories can be efficient alternatives to chemical catalysts that have been used to synthesize organic molecules. However, the design of artificial enzymes is challenging and requires a detailed molecular-level analysis to understand the mechanism they promote in order to design efficient variants. In this study, we computationally investigate the mechanism of proficient Morita-Baylis-Hillman enzymes developed using a combination of computational design and directed evolution. The powerful transition path sampling method coupled with in-depth post-processing analysis has been successfully used to elucidate the different chemical pathways, transition states, protein dynamics, and free energy barriers of reactions catalyzed by such laboratory-optimized enzymes. This research provides an explanation for how different chemical modifications in an enzyme affect its catalytic activity in ways that are not predictable by static design algorithms.

Longitudinal Follow-Up of Children With HLHS and Association Between Norwood Shunt Type and Long-Term Outcomes: The SVR III Study.

OBJECTIVE: In the SVR trial (Single Ventricle Reconstruction), newborns with hypoplastic left heart syndrome were randomly assigned to receive a modified Blalock-Taussig-Thomas shunt (mBTTS) or a right ventricle-to-pulmonary artery shunt (RVPAS) at Norwood operation. Transplant-free survival was superior in the RVPAS group at 1 year, but no longer differed by treatment group at 6 years; both treatment groups had accumulated important morbidities. In the third follow-up of this cohort (SVRIII [Long-Term Outcomes of Children With Hypoplastic Left Heart Syndrome and the Impact of Norwood Shunt Type]), we measured longitudinal outcomes and their risk factors through 12 years of age. METHODS: Annual medical history was collected through record review and telephone interviews. Cardiac magnetic resonance imaging (CMR), echocardiogram, and cycle ergometry cardiopulmonary exercise tests were performed at 10 through 14 years of age among participants with Fontan physiology. Differences in transplant-free survival and complication rates (eg, arrhythmias or protein-losing enteropathy) were identified through 12 years of age. The primary study outcome was right ventricular ejection fraction (RVEF) by CMR, and primary analyses were according to shunt type received. Multivariable linear and Cox regression models were created for RVEF by CMR and post-Fontan transplant-free survival. RESULTS: Among 549 participants enrolled in SVR, 237 of 313 (76%; 60.7% male) transplant-free survivors (mBTTS, 105 of 147; RVPAS, 129 of 161; both, 3 of 5) participated in SVRIII. RVEF by CMR was similar in the shunt groups (RVPAS, 51±9.6 [n=90], and mBTTS, 52±7.4 [n=75]; P=0.43). The RVPAS and mBTTS groups did not differ in transplant-free survival by 12 years of age (163 of 277 [59%] versus 144 of 267 [54%], respectively; P=0.11), percentage predicted peak Vo2 for age and sex (74±18% [n=91] versus 72±18% [n=84]; P=0.71), or percentage predicted work rate for size and sex (65±20% versus 64±19%; P=0.65). The RVPAS versus mBTTS group had a higher cumulative incidence of protein-losing enteropathy (5% versus 2%; P=0.04) and of catheter interventions (14 versus 10 per 100 patient-years; P=0.01), but had similar rates of other complications. CONCLUSIONS: By 12 years after the Norwood operation, shunt type has minimal association with RVEF, peak Vo2, complication rates, and transplant-free survival. RVEF is preserved among the subgroup of survivors who underwent CMR assessment. Low transplant-free survival, poor exercise performance, and accruing morbidities highlight the need for innovative strategies to improve long-term outcomes in patients with hypoplastic left heart syndrome. REGISTRATION: URL: https://www. CLINICALTRIALS: gov; Unique identifier: NCT0245531.

Reintervention Before Bidirectional Cavopulmonary Shunt and Intermediate Outcomes in Children with Single Ventricle Who Underwent Main Pulmonary Artery Banding.

Unplanned reinterventions following pulmonary artery banding (PAB) in single ventricle patients are common before stage 2 palliation (S2P) but associated risk factors are unknown. We hypothesized that reintervention is more common when PAB is placed at younger age and with a looser band, reflected by lower PAB pressure gradient. Retrospective single center study of single ventricle patients undergoing PAB between Jan 2000 and Dec 2020. The association with reintervention and successful S2P was modeled using exploratory cause-specific hazard regression. A multivariable model was developed adjusting for clinical and statistically relevant predictors. The cumulative proportion of patients undergoing reintervention were summarized using a competing risk model. 77 patients underwent PAB at median (IQR) 47 (24-66) days and 3.73 (3.2-4.5) kg. Within18 months of PAB, 60 (78%) reached S2P, 9 (12%) died, 1 (1%) transplanted and 7 (9%) were alive without S2P. Within 18 months of PAB 10 (13%) patients underwent reintervention related to pulmonary blood flow modification: PAB adjustment (n = 6) and conversion to Damus-Kaye-Stansel/Blalock-Taussig-Thomas shunt (n = 4). 6/10 (60%) reached S2P following reintervention. A trend toward higher intervention in patients with a genetic syndrome (p-0.06) and weight < 3 kg (p-0.057) at time of PAB was noted. Only genetic syndrome was a risk factor associated with poor outcome (p-0.025). PAB has a reasonable outcome in SV patients with unobstructed systemic and pulmonary blood flow, but with a high reintervention rate. Only a quarter of patients with genetic syndromes reach S2P and further study is required to explore the benefits from an alternative palliative strategy.

Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling.

Despite initial resistance, it has been increasingly accepted that protein dynamics plays a role in enzymatic catalysis. There have been two lines of research. Some works study slow conformational motions that are not coupled to the reaction coordinate, but guide the system towards catalytically competent conformations. Understanding at the atomistic level how this is accomplished has remained elusive except for a few systems. In this review we focus on fast sub-picosecond motions that are coupled to the reaction coordinate. The use of Transition Path Sampling has allowed us an atomistic description of how these rate-promoting vibrational motions are incorporated in the reaction mechanism. We will also show how we used insights from rate-promoting motions in protein design.

Protein Dynamics and Enzymatic Catalysis.

This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.

Frosted Branch Angiitis in the Setting of Active COVID-19 Infection and Underlying Mixed Connective Tissue Disease.

Frosted branch angiitis (FBA) is an uncommon form of retinal vasculitis and is typically associated with vision loss. We report a unique case of FBA that manifested in the setting of an active COVID-19 infection in a patient with Mixed Connective Tissue Disease (MCTD). A 34-year-old female with a history of MCTD, including overlapping findings of dermatomyositis, systemic lupus erythematosus, and rheumatoid arthritis, on immunosuppressive medications, presented for left-sided vision loss. She was also found to have an active COVID-19 infection with symptoms including sore throat and dry cough. The patient's visual acuity was counting fingers in her affected eye with a fundus exam revealing diffuse retinal hemorrhages, retinal whitening, cystoid macular edema, and perivascular sheathing of tertiary arterioles and venules, characteristic of FBA. Labs showed mildly elevated inflammatory markers. She exhibited no other signs or symptoms concerning systemic rheumatologic flare. There was no evidence of COVID-19 on viral PCR testing of intraocular fluid but given her positive nasopharyngeal PCR, COVID-induced retinal vasculitis with FBA remained high on the differential. The patient's retinal vasculitis later improved with heightened immunosuppressive therapy including high-dose intravenous corticosteroids. Clinicians should be aware of the possibility of COVID-related FBA, particularly in patients with an underlying predisposition to autoimmune inflammation. Our experience with this patient highlights the utility of high-dose systemic immunosuppressive therapy in treating such inflammatory occlusive retinal vasculitis. Further studies are needed to characterize retinal manifestations of COVID-19 in the setting of autoimmune disease.

Methods to Enhance Causal Inference for Assessing Impact of Clinical Informatics Platform Implementation.

BACKGROUND: Hospitals are increasingly likely to implement clinical informatics tools to improve quality of care, necessitating rigorous approaches to evaluate effectiveness. We leveraged a multi-institutional data repository and applied causal inference methods to assess implementation of a commercial data visualization software in our pediatric cardiac intensive care unit. METHODS: Natural experiment in the University of Michigan (UM) Cardiac Intensive Care Unit pre and postimplementation of data visualization software analyzed within the Pediatric Cardiac Critical Care Consortium clinical registry; we identified N=21 control hospitals that contributed contemporaneous registry data during the study period. We used the platform during multiple daily rounds to visualize clinical data trends. We evaluated outcomes-case-mix adjusted postoperative mortality, cardiac arrest and unplanned readmission rates, and postoperative length of stay-most likely impacted by this change. There were no quality improvement initiatives focused specifically on these outcomes nor any organizational changes at UM in either era. We performed a difference-in-differences analysis to compare changes in UM outcomes to those at control hospitals across the pre versus postimplementation eras. RESULTS: We compared 1436 pre versus 779 postimplementation admissions at UM to 19 854 (pre) versus 14 160 (post) at controls. Admission characteristics were similar between eras. Postimplementation at UM we observed relative reductions in cardiac arrests among medical admissions, unplanned readmissions, and postoperative length of stay by -14%, -41%, and -18%, respectively. The difference-in-differences estimate for each outcome was statistically significant (P<0.05), suggesting the difference in outcomes at UM pre versus postimplementation is statistically significantly different from control hospitals during the same time. CONCLUSIONS: Clinical registries provide opportunities to thoroughly evaluate implementation of new informatics tools at single institutions. Borrowing strength from multi-institutional data and drawing ideas from causal inference, our analysis solidified greater belief in the effectiveness of this software across our institution.

Classical Molecular Dynamics Simulation of Glyonic Liquids: Structural Insights and Relation to Conductive Properties.

Rhamnolipids are biosurfactants that have obtained wide industrial and environmental interests with their biodegradability and great surface activity. Besides their important roles as surfactants, they are found to function as a new type of glycolipid-based protic ionic liquids (ILs)─glyonic liquids (GLs). GLs are reported to have impressive physicochemical properties, especially superionic conductivity, and it was reported in experiments that specific ion selections and the fraction of water content have a strong effect on the conductivity. Also, the shape of the conductivity curve as a function of water fraction in GLs is interesting with a sharp increase first and a long plateau. We related the conductivities to the three-dimensional (3D) networks composed of -OH inside the GLs utilizing classical molecular dynamics (MD) simulations. The amount and size of these networks vary with both ion species and water fractions. Before reaching the first hydration layer, the -OH networks with higher projection/box length ratios indicate better conductivity; after reaching the first hydration layer and forming continuous structures, the conductivity retains with more water molecules participating in the continuous networks. Therefore, networks are found to be a qualitative predictor of actual conductivity. This is explained by the analysis of the atomic structures, including radial distribution function, fraction free volume, anion conformations, and hydrogen bond occupancies, of GLs and their water mixtures under different chemical conditions.

Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase.

The influence of protein motions on enzyme catalysis remains a topic of active discussion. Protein motions occur across a variety of time scales, from vibrational fluctuations in femtoseconds, to collective motions in milliseconds. There have been numerous studies that show conformational motions may assist in catalysis, protein folding, and substrate specificity. It is also known through transition path sampling studies that rapid promoting vibrations contribute to enzyme catalysis. Human purine nucleoside phosphorylase (PNP) is one enzyme that contains both an important conformational motion and a rapid promoting vibration. The slower motion in this enzyme is associated with a loop motion, that when open allows substrate entry and product release but closes over the active site during catalysis. We examine the differences between an unconstrained PNP structure and a PNP structure with constraints on the loop motion. To investigate possible coupling between the slow and fast protein dynamics, we employed transition path sampling, reaction coordinate identification, electric field calculations, and free energy calculations reported here.

Development of the Residual Lesion Score for congenital heart surgery: the RAND Delphi methodology.

BACKGROUND AND OBJECTIVE: The Residual Lesion Score is a novel tool for assessing the achievement of surgical objectives in congenital heart surgery based on widely available clinical and echocardiographic characteristics. This article describes the methodology used to develop the Residual Lesion Score from the previously developed Technical Performance Score for five common congenital cardiac procedures using the RAND Delphi methodology. METHODS: A panel of 11 experts from the field of paediatric and congenital cardiology and cardiac surgery, 2 co-chairs, and a consultant were assembled to review and comment on validity and feasibility of measuring the sub-components of intraoperative and discharge Residual Lesion Score for five congenital cardiac procedures. In the first email round, the panel reviewed and commented on the Residual Lesion Score and provided validity and feasibility scores for sub-components of each of the five procedures. In the second in-person round, email comments and scores were reviewed and the Residual Lesion Score revised. The modified Residual Lesion Score was scored independently by each panellist for validity and feasibility and used to develop the "final" Residual Lesion Score. RESULTS: The Residual Lesion Score sub-components with a median validity score of ≥7 and median feasibility score of ≥4 that were scored without disagreement and with low absolute deviation from the median were included in the "final" Residual Lesion Score. CONCLUSION: Using the RAND Delphi methodology, we were able to develop Residual Lesion Score modules for five important congenital cardiac procedures for the Pediatric Heart Network's Residual Lesion Score study.

Insights into the Mechanism of the Cardiac Drug Omecamtiv Mecarbil─A Computational Study.

Omecamtiv mecarbil (OM) is a positive inotrope that is thought to bind directly to an allosteric site of the ß-cardiac myosin. The drug is under investigation for the treatment of systolic heart failure. The drug is classified as a cardiac myosin modulator and has been observed to affect multiple vital steps of the cross-bridge cycle including the recovery stroke and the chemical step. We explored the free-energy surface of the recovery stroke of the human cardiac ß-myosin in the presence of OM to determine its influence on this process. We also investigated the effects of OM on the recovery stroke in the presence of genetic cardiomyopathic mutations R712L, F764L, and P710R using metadynamics. We also utilized the method of transition path sampling to generate an unbiased ensemble of reactive trajectories for the ATP hydrolysis step in the presence of OM that were able to provide insight into the differences observed due to OM in the dynamics and mechanism of the decomposition of ATP to ADP and HPO42-, a central part of the power generation in cardiac muscle. We studied chemistry in the presence of the same three mutations to further elucidate the effect of OM, and its use in the treatment of cardiac disease.

Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.

This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.

Bipolar Electric Field Pulses in the Martian Magnetosheath and Solar Wind; Their Implication and Impact Accessed by System Scale Size.

The scale size of the plasma boundary region between the sheath and ionosphere in the Martian system is often similar to the gyro-radii of sheath protons, ∼200 km. As a result, ion energization via kinetic structures may play an important role in modifying the ion trajectories and thus be important when evaluating the large-scale dynamics of the Martian system. In this paper, we report observations made with the MAVEN Langmuir Probe and Waves instrument of solitary bipolar electric field structures, and assess their potential role in ion energization in the Martian system. The observed structures appear as short duration (∼0.5 ms) bipolar electric field pulses of ∼1-25 mV/m, and are frequently observed in the upstream solar wind and inside the sheath. The study presented in this paper suggests that the bipolar electric field structures observed at Mars have an average electrostatic potential drop of ∼0.07 V. The estimated upper rate at which these structures could further energize the protons is estimated, assuming the protons gain the full 0.07 eV, to be ∼0.13 eV per gyration, or a change in proton energy of ∼0.3%, and a corresponding change in the gyroradius of ∼0.3 km. These numbers imply that to first order the bipolar structures are not a significant source of ion energization in the Martian magnetosheath.

The pediatric heart network's study on long-term outcomes of children with HLHS and the impact of Norwood Shunt type in the single ventricle reconstruction trial cohort (SVRIII): Design and adaptations.

BACKGROUND: The Single Ventricle Reconstruction (SVR) Trial was the first randomized clinical trial of a surgical approach for treatment of congenital heart disease. Infants with hypoplastic left heart syndrome (HLHS) and other single right ventricle (RV) anomalies were randomized to a modified Blalock Taussig Thomas shunt (mBTTS) or a right-ventricular-to-pulmonary-artery shunt (RVPAS) at the time of the Norwood procedure. The aim of the Long-term Outcomes of Children with HLHS and the Impact of Norwood Shunt Type (SVR III) study is to compare early adolescent outcomes including measures of cardiac function, transplant-free survival, and neurodevelopment, between those who received a mBTTS and those who received an RVPAS. METHODS: Transplant-free survivors of the SVR cohort were enrolled at 10 to 15 years of age for multifaceted in-person evaluation of cardiac function (cardiac magnetic resonance [CMR], echocardiogram and exercise test) and neurodevelopmental evaluation. Right ventricular ejection fraction measured by CMR served as the primary outcome. Development of arrhythmias, protein losing enteropathy, and other comorbidities were assessed through annual medical history interview. Through the course of SVR III, protocol modifications to engage SVR trial participants were designed to enhance recruitment and retention. CONCLUSIONS: Evaluation of long-term outcomes will provide important data to inform decisions about the shunt type placed at the Norwood operation and will improve the understanding of cardiovascular and neurodevelopmental outcomes for early adolescents with HLHS.

Analyzing Continuous Physiologic Data to Find Hemodynamic Signatures Associated With New Brain Injury After Congenital Heart Surgery.

Continuous data capture technology is becoming more common. Establishing analytic approaches for continuous data could aid in understanding the relationship between physiology and clinical outcomes. OBJECTIVES: Our objective was to design a retrospective analysis for continuous physiologic measurements and their relationship with new brain injury over time after cardiac surgery. DESIGN SETTING AND PARTICIPANTS: Retrospective cohort study in the Cardiac Critical Care Unit at the Hospital for Sick Children in patients after repair of transposition of the great arteries (TGA) or single ventricle (SV) lesions. MAIN OUTCOMES AND MEASURES: Continuously acquired physiologic measurements for up to 72 hours after cardiac surgery were analyzed for association with new brain injury by MRI. Distributions of heart rate (HR), systolic blood pressure (BP), and oxygen saturation (Spo2) for SV and TGA were analyzed graphically and with descriptive statistics over postoperative time for data-driven variable selection. Mixed-effects regression analyses characterized relationships between HR, BP, and Spo2 and new brain injury over time while accounting for variation between patients, measurement heterogeneity, and missingness. RESULTS: Seventy-seven patients (60 TGA; 17 SV) were included. New brain injury was seen in 26 (34%). In SV patients, with and without new brain injury, respectively, in the first 24 hours after cardiac surgery, the median (interquartile range) HR was 172.0 beats/min (bpm) (169.7-176.0 bpm) versus 159.6 bpm (145.0-167.0 bpm); systolic BP 74.8 (67.9-78.5 mm Hg) versus 68.9 mm Hg (61.6-70.9 mm Hg). Higher postoperative HR (parameter estimate, 19.4; 95% CI, 7.8-31; p = 0.003 and BP, 8.6; 1.3-15.8; p = 0.024) were associated with new brain injury in SV patients. The strength of this relationship decreased with time. CONCLUSIONS AND RELEVANCE: Retrospective analysis of continuous physiologic measurements can provide insight into changes in postoperative physiology over time and their relationship with new brain injury. This technique could be applied to assess relationships between physiologic data and many patient interventions or outcomes.

Transition Path Sampling Based Calculations of Free Energies for Enzymatic Reactions: The Case of Human Methionine Adenosyl Transferase and Plasmodium vivax Adenosine Deaminase.

Transition path sampling (TPS) is widely used for the calculations of reaction rates, transition state structures, and reaction coordinates of condensed phase systems. Here we discuss a scheme for the calculation of free energies using the ensemble of TPS reactive trajectories in combination with a window-based sampling technique for enzyme-catalyzed reactions. We calculate the free energy profiles of the reactions catalyzed by the human methionine S-adenosyltransferase (MAT2A) enzyme and the Plasmodium vivax adenosine deaminase (pvADA) enzyme to assess the accuracy of this method. MAT2A catalyzes the formation of S-adenosine-l-methionine following a SN2 mechanism, and using our method, we estimate the free energy barrier for this reaction to be 16 kcal mol-1, which is in excellent agreement with the experimentally measured activation energy of 17.27 kcal mol-1. Furthermore, for the pvADA enzyme-catalyzed reaction we estimate a free energy barrier of 21 kcal mol-1, and the calculated free energy profile is similar to that predicted from experimental observations. Calculating free energies by employing our simple method within TPS provides significant advantages over methods such as umbrella sampling because it is free from any applied external bias, is accurate compared to experimental measurements, and has a reasonable computational cost.