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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.

Omecamtiv mecarbil (OM) is a positive inotrope that is thought to bind directly to an allosteric site of the β-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 β-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 HPO

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

The troponin core is an important regulatory complex in cardiac sarcomeres. Contraction is initiated by a calcium ion binding to cardiac troponin C (cTnC), initiating a conformational shift within the protein, altering its interactions with cardiac troponin I (cTnI). The change in cTnC–cTnI interactions prompts the C-terminal domain of cTnI to dissociate from actin, allowing tropomyosin to reveal myosin-binding sites on actin. Each of the concerted movements in the cardiac thin filament (CTF) is crucial for allowing the contraction of cardiomyocytes, yet little is known about the free energy associated with each transition, which is vital for understanding contraction on a molecular level. Using metadynamics, we calculated the free-energy surface of two transitions in the CTF: cTnC opening in the presence and absence of Ca(2+) and cTnI dissociating from actin with both open and closed cTnC. These results not only provide the free-energy surface of the transitions but will also be shown to determine if the order of transitions in the contraction cycle is important. From our calculations, we found that the calcium ion helps stabilize the open conformation of cTnC and that the C-terminus of cTnI is stabilized by cTnC in the open conformation when dissociating from the actin surface.

Simulation methods like transition path sampling (TPS) generate an abundance of information buried in the collection of reactive trajectories that they generate. However, only limited use has been made of this information, mainly for the identification of the reaction coordinate. The standard TPS tools have been designed for monitoring the progress of the system from reactants to products. However, the reaction coordinate does not contain all the information regarding the mechanism. In our earlier work, we have used TPS on enzymatic systems and have identified important motions in the reactant well that prepares the system for the reaction. Since these events take place in the reactant well, they are beyond the reach of standard TPS postprocessing methods. We present a simple scheme for identifying the common trends in enzymatic trajectories. This scheme was designed for a specific class of enzymatic reactions: it can be used for identifying motions that guide the system to reaction-ready conformations. We have applied it to two enzymatic systems that we have studied in the past, formate dehydrogenase and purine nucleoside phosphorylase, and we were able to identify interactions, far from the transition state, that are important for preparing the system for the reaction but that had been overlooked in earlier work.

To evaluate the mid-term outcomes of pars plana vitrectomy performed for retinal detachment (RD) repair after Boston Type 1 keratoprosthesis (KPro) implantation.Retrospective review of medical records of KPro implanted at the Stein Eye Institute presenting with RD and treated by pars plana vitrectomy. Functional success was defined as a postoperative visual acuity maintained within 2 Snellen lines of the corrected distance visual acuity measured before the development of the RD (baseline) and anatomical success as an attached retina after the pars plana vitrectomy. Kaplan-Meyer survival analyses were performed.Among the 224 KPro performed, 28 (15.2%) RD were identified; of which, 21 (9.4%) were included. The mean follow-up was 42.5 ± 27.3 months. Vitreoretinal proliferation was present in 18 of 21 eyes (85.7%). Surgical techniques were adapted to the complex anterior segment anatomy of KPro eyes. Anatomical success was achieved in 18 of 21 eyes (85.7%). Functional success occurred in 17 of 21 eyes (81.0%), and 5 of 21 eyes (23.8%) reached 20/400 or better visual acuity at the final follow-up. The KPro was retained in 11 in 21 eyes (52.4%). The retention rate decreased from 94.7% at 1 year to 53.5% at 5 years. The most frequent complications were retroprosthetic membrane (47.6%) and corneal melt (23.8%).Modified pars plana vitrectomy techniques resulted in relatively good mid-term anatomical, functional, and retention rate outcomes, given the severity of RD at presentation and the numerous preoperative comorbidities of KPro eyes.

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.

To determine the characteristics and appearance rate of epiretinal proliferation (ERP) on SD-OCT after surgery for rhegmatogenous retinal detachment (RRD) repair. One hundred eight eyes of 108 patients who underwent one or more surgeries for RRD were enrolled. The eyes with other maculopathies that were directly related to RRD were excluded. Image acquisition was performed with SD-OCT (Heidelberg Engineering, Germany). Clinical charts were reviewed to assess clinical and surgical findings. Statistical analyses were performed using XLSTAT (Assinsoft, Paris, France). ERP was found in 9.3% eyes (n = 10). The mean initial visual acuity (logMAR) was 1.34 ± 0.82 in the ERP group compared to 0.49 ± 0.70 in the non-ERP group. PVR was present in 70.0% and chronic macular edema was found in 80.0% of eyes which developed ERP. The mean number of vitreoretinal surgeries in eyes with ERP was 3.3 ± 1.19 and only 1.44 ± 1.02 in eyes without. Silicone oil was used in 60.0% of eyes which developed ERP compared to 13.9% in the non-ERP group. ERP is a late-onset postoperative finding in eyes with RRD and can occur in absence of macular holes. Overall, ERP is more frequent in eyes with complicated courses of RRD including multiple operations, PVR, usage of silicone oil, and chronic macular edema.

Purpose To define injection index (II) and assess its impact on visual acuity (VA) in pigment epithelial detachment from age-related macular degeneration over 5 years. Methods Injection index is defined as the mean anti-vascular endothelial growth factor injections per year from presentation. A retrospective study of 256 eyes in 213 patients was performed. Patients were stratified by II (high: ≥9, low: Results Baseline characteristics showed no differences across II groups. Mean (range) follow-up, in years, was 5.02 (1.04-12.74) for all patients. Mean logMAR VA (Snellen VA) were 0.60 (20/80) and 0.56 (20/73) at baseline, 0.52 (20/66) and 0.59 (20/78) at Year 1, 0.45 (20/56) and 0.67 (20/94) at Year 2, 0.38 (20/48) and 0.66 (20/91) at Year 3, 0.41 (20/51) and 0.89 (20/155) at Year 4, and 0.35 (20/45) and 0.79 (20/123) at Year 5 for the high and low II groups, respectively. Linear regression analysis showed a gain of 0.5 approxETDRS letters with each additional injection per year. Conclusion Increased II was associated with better mean VA, suggesting that long-term continuous vascular endothelial growth factor suppression may improve VA in eyes thought to carry poor prognoses.

Human cardiac β myosin undergoes the crossbridge cycle as part of the force-generating mechanism of cardiac muscle. The recovery stroke is considered one of the key steps of the kinetic cycle as it is the conformational rearrangement required to position the active site residues for hydrolysis of ATP and interaction with actin. We explored the free-energy surface of the transition and investigated the effect of the genetic cardiomyopathy causing mutations R453C, I457T, and I467T on this step using metadynamics. This work extends previous studies on Dictyostelium myosin II with engineered mutations. Here, like previously, we generated an unbiased thermodynamic ensemble of reactive trajectories for the chemical step using transition path sampling. Our methodologies were able to predict the changes to the dynamics of the recovery stroke as well as predict the pathway of breakdown of ATP to ADP and HPO(4)(2−) with the stabilization of the metaphosphate intermediate. We also observed clear differences between the Dictyostelium myosin II and human cardiac β myosin for ATP hydrolysis as well as predict the effect of the mutation I467T on the chemical step.

The movement of tropomyosin over filamentous actin regulates the cross-bridge cycle of the thick with thin filament of cardiac muscle by blocking and revealing myosin binding sites. Tropomyosin exists in three, distinct equilibrium states with one state blocking myosin-actin interactions (blocked position) and the remaining two allowing for weak (closed position) and strong myosin binding (open position). However, experimental information illuminating how myosin binds to the thin filament and influences tropomyosin’s transition across the actin surface is lacking. Using metadynamics, we mimic the effect of a single myosin head binding by determining the work required to pull small segments of tropomyosin toward the open position in several distinct regions of the thin filament. We find differences in required work due to the influence of cardiac troponin T lead to preferential binding sites and determine the mechanism of further myosin head recruitment.

The retinal vasculature provides important clues in the diagnosis and monitoring of systemic diseases including hypertension and diabetes. The microvascular system is of primary involvement in such conditions, and the retina is the only anatomical site where the microvasculature can be directly observed. The objective assessment of retinal vessels has long been considered a surrogate biomarker for systemic vascular diseases, and with recent advancements in retinal imaging and computer vision technologies, this topic has become the subject of renewed attention. In this paper, we present a novel dataset, dubbed RAVIR, for the semantic segmentation of Retinal Arteries and Veins in Infrared Reflectance (IR) imaging. It enables the creation of deep learning-based models that distinguish extracted vessel type without extensive post-processing. We propose a novel deep learning-based methodology, denoted as SegRAVIR, for the semantic segmentation of retinal arteries and veins and the quantitative measurement of the widths of segmented vessels. Our extensive experiments validate the effectiveness of SegRAVIR and demonstrate its superior performance in comparison to state-of-the-art models. Additionally, we propose a knowledge distillation framework for the domain adaptation of RAVIR pretrained networks on color images. We demonstrate that our pretraining procedure yields new state-of-the-art benchmarks on the DRIVE, STARE, and CHASE_DB1 datasets. Dataset link: https://ravirdataset.github.io/data/, Comment: Paper accepted to IEEE Journal of Biomedical Health Informatics (JBHI)

To describe the clinical characteristics and visual outcomes of neovascular age-related macular degeneration (NV-AMD) patients with irregular pigment epithelium detachment (PED) and non-resolving subretinal fluid (SRF) despite continuous monthly injections of anti-vascular endothelial growth factor (VEGF). This is a retrospective case series, including NV-AMD patients treated in a tertiary academic practice. Inclusion criteria were NV-AMD diagnosis, with irregular PED, and non-resolving SRF treated with continuous monthly anti-VEGF intravitreal injections. Data collection included best corrected visual acuity (BCVA), central macular thickness (CMT), sub-foveal choroidal thickness (SFCT), and type and location of PED as seen on optical coherence tomography (OCT). A total of 738 patients with NV-AMD underwent anti-VEGF injections during the follow-up period and 20 eyes of 19 patients (14 females and 5 males) met the inclusion criteria. Average age was 81.7 ± 6.6 years, mean follow-up time was 32.1 ± 23.5 months, and mean number of injections was 31.3 ± 24.2. Mean VA was 0.26 ± 0.21 logMAR (Snellen 20/36) at baseline versus 0.20 ± 0.23 logMAR (Snellen 20/32) at the end of the follow-up (P = 0.28). All eyes presented with sub-foveal, type 1 macular neovascularization (MNV). Average sub-foveal choroidal thickness changed from 189.70 ± 68.46 μm at baseline to 169.00 ± 63.06 μm (P

Myosin regulates muscle function through a complex cycle of conformational rearrangements coupled with the hydrolysis of adenosine triphosphate (ATP). The recovery stroke reorganizes the myosin active site to hydrolyze ATP and cross bridge with the thin filament to produce muscle contraction. Engineered mutations K84M and R704E in Dictyostelium myosin have been designed to specifically inhibit the recovery stroke and have been shown to indirectly affect the ATPase activity of myosin. We investigated these mutagenic perturbations to the recovery stroke and generated thermodynamically correct and unbiased trajectories for native ATP hydrolysis with computationally enhanced sampling methods. Our methodology was able to resolve experimentally observed changes to kinetic and equilibrium dynamics for the recovery stroke with the correct prediction in the severity of these changes. For ATP hydrolysis, the sequential nature along with the stabilization of a metaphosphate intermediate was observed in agreement with previous studies. However, we observed glutamate 459 being utilized as a proton abstractor to prime the attacking water instead of a lytic water, a phenomenon not well categorized in myosin but has in other ATPases. Both rare event methodologies can be extended to human myosin to investigate isoformic differences from Dictyostelium and scan cardiomyopathic mutations to see differential perturbations to kinetics of other conformational changes in myosin such as the power stroke.

We have analyzed the reaction catalyzed by formate dehydrogenase using transition path sampling. This system has recently received experimental attention using infrared spectroscopy and heavy-enzyme studies. Some of the experimental results point to the possible importance of protein motions that are coupled to the chemical step. We found that the residue Val123 that lies behind the nicotinamide ring occasionally comes into van der Waals contact with the acceptor and that in all reactive trajectories, the barrier-crossing event is preceded by this contact, meaning that the motion of Val123 is part of the reaction coordinate. Experimental results have been interpreted with a two-dimensional formula for the chemical rate, which cannot capture effects such as the one we describe.

Morphinone reductase (MR) is an important model system for studying the contribution of protein motions to H-transfer reactions. In this research, we used quantum mechanical/molecular mechanics (QM/MM) simulation together with transition path sampling (TPS) simulation to study two important topics of current research on MR: the existence of multiple catalytic reaction pathways and the involvement of fast protein motions in the catalytic process. We have discovered two reaction pathways for the wild type and three reaction pathways for the N189A mutant. With the committor distribution analysis method, we found reaction coordinates for all five reaction pathways. Only one wild-type reaction pathway has a rate-promoting vibration from His186, while all of the other four pathways do not involve any protein motions in their catalytic process through the transition state. The rate-promoting vibration in the wild-type MR, which comes from a direction perpendicular to the donor-acceptor axis, functions to decrease the donor-acceptor distance by causing a subtle "out-of-plane" motion of a donor atom. By comparing reaction pathways between the two enzymes, we concluded that the major effect of the N189A point mutation is to increase the active site volume by altering the active site backbone and eliminating the Asn189 side chain. This effect causes a different NADH geometry at the reactant state, which very well explains the different reaction mechanisms between the two enzymes, as well as the disappearance of the His186 rate-promoting vibrations in the N189A mutant. The unfavorable geometry of the NADH pyridine ring induced by the N189A point mutation is the potential cause of multiple reaction pathways in N189A mutants.

Protein engineering is a growing field with a variety of experimental techniques available for altering protein function. However, creating an enzyme de novo is still in its infancy, so far yielding enzymes of modest catalytic efficiency. In this study, a system of artificial retro-aldolase enzymes found to have chemistry coupled to protein dynamics was examined. The original design was created computationally, and this protein was then subjected to directed evolution to improve the initial low catalytic efficiency. We found that this re-engineering of the enzyme resulted in rapid density fluctuations throughout the enzyme being reshaped via alterations in the hydrogen bonding network. This work also led to the discovery of a second important motion which aids in the release of an intermediate product. These results provide compelling evidence that to engineer efficient protein catalysts, fast protein dynamics need to be considered in the design.

Ultra-widefield fundus autofluorescence imaging reveals abnormalities in degenerative retinoschisis that allow for the identification of an associated neurosensory detachment confirmed by spectral domain optical coherence tomography., Purpose: To determine whether neurosensory retinal detachment complicating degenerative retinoschisis (RS) can be reliably detected with ultra-widefield fundus autofluorescence evaluation. Methods: Consecutive patients diagnosed with RS who had ultra-widefield fundus autofluorescence imaging were included in this retrospective case series. According to the fundus autofluorescence patterns, we divided the eyes into two groups: 1) eyes with RS and a hyperautofluorescent leading edge and 2) eyes with RS and without hyperautofluorescence. Peripheral spectral domain optical coherence tomography images at the level of RS were obtained. Results: Thirty-eight eyes that met eligibility criteria were identified. Review of ultra-widefield fundus autofluorescence demonstrated 21/39 (55%) eyes with distinctive hyperautofluorescence over the area of RS (Group A) and 17/38 (45%) eyes without any form of hyperautofluorescence (Group B). Spectral domain optical coherence tomography images confirmed the presence of full-thickness neurosensory retina separation from the underlying retinal pigment epithelium in the areas of hyperautofluorescence in 10/10 eyes (100%) from Group A. None (0/11; 0%) of the eyes from Group B showed full-thickness neurosensory retina separation on the spectral domain optical coherence tomography imaging of the retina–RS interface. Conclusion: Hyperautofluorescent findings suggest the presence of a neurosensory retinal detachment. Retinal detachment associated with RS can be reliably detected on ultra-widefield fundus autofluorescence and may be a useful diagnostic imaging modality.

Purpose: This article illustrates multiple atypical manifestations of ocular toxoplasmosis masquerading as acute retinal necrosis and vitreoretinal lymphoma. Methods: Two case presentations are discussed, and the body of pertinent literature is reviewed and discussed. Results: In these cases, an extensive workup and attention to history lead to the correct diagnosis and management. Conclusions: Aggressive cases of ocular toxoplasmosis may present in a variety of phenotypes that may mimic other vision- and potentially life-threatening conditions, particularly in a milieu of inadequate endogenous and exogenous antimicrobial defenses.

Heavy enzyme isotope effects occur in proteins substituted with (2)H-, (13)C-, and (15)N-enriched amino acids. Mass alterations perturb femtosecond protein motions and have been used to study the linkage between fast motions and transition-state barrier crossing. Heavy enzymes typically show slower rates for their chemical steps. Heavy bacterial methylthioadenosine nucleosidases (MTANs from Helicobactor pylori and Escherichia coli) gave normal isotope effects in steady-state kinetics, with slower rates for the heavy enzymes. However, both enzymes revealed rare inverse isotope effects on their chemical steps, with faster chemical steps in the heavy enzymes. Computational transition-path sampling studies of H. pylori and E. coli MTANs indicated closer enzyme–reactant interactions in the heavy MTANs at times near the transition state, resulting in an improved reaction coordinate geometry. Specific catalytic interactions more favorable for heavy MTANs include improved contacts to the catalytic water nucleophile and to the adenine leaving group. Heavy bacterial MTANs depart from other heavy enzymes as slowed vibrational modes from the heavy isotope substitution caused improved barrier-crossing efficiency. Improved sampling frequency and reactant coordinate distances are highlighted as key factors in MTAN transition-state stabilization.

To determine the characteristics and appearance rate of epiretinal proliferation (ERP) on SD-OCT after surgery for rhegmatogenous retinal detachment (RRD) repair.One hundred eight eyes of 108 patients who underwent one or more surgeries for RRD were enrolled. The eyes with other maculopathies that were directly related to RRD were excluded. Image acquisition was performed with SD-OCT (Heidelberg Engineering, Germany). Clinical charts were reviewed to assess clinical and surgical findings. Statistical analyses were performed using XLSTAT (Assinsoft, Paris, France).ERP was found in 9.3% eyes (n = 10). The mean initial visual acuity (logMAR) was 1.34 ± 0.82 in the ERP group compared to 0.49 ± 0.70 in the non-ERP group. PVR was present in 70.0% and chronic macular edema was found in 80.0% of eyes which developed ERP. The mean number of vitreoretinal surgeries in eyes with ERP was 3.3 ± 1.19 and only 1.44 ± 1.02 in eyes without. Silicone oil was used in 60.0% of eyes which developed ERP compared to 13.9% in the non-ERP group.ERP is a late-onset postoperative finding in eyes with RRD and can occur in absence of macular holes. Overall, ERP is more frequent in eyes with complicated courses of RRD including multiple operations, PVR, usage of silicone oil, and chronic macular edema.

For decades, there has been debate regarding the origin of the catalytic power of enzymes. In this work, we use the approach of computational chemistry to study the enzyme catechol O-methyltransferase (COMT) and reveal that the two current views on the catalytic mechanism of enzymes, the rate-promoting vibrations and the electric field, may both be viewed as part of the chemical step catalyzed by COMT. However, we show that the rate-promoting vibrations cause the electrostatic effect. This work provides insight into the catalytic mechanism of COMT and resolves a longstanding controversy regarding this enzyme’s mechanism.

Purpose To investigate risk factors, imaging characteristics, and treatment responses of cystoid macular edema (CME) after rhegmatogenous retinal detachment (RRD) repair. Methods Consecutive, retrospective case–control series of patients who underwent pars plana vitrectomy (PPV) and/or scleral buckling (SB) for RRD, with at least six months of follow-up. Clinical and surgical parameters of patients with and without CME (nCME), based on spectral-domain optical coherence tomography (OCT), were compared. Results Of 99 eyes enrolled, 25 had CME while 74 had nCME. Patients with CME underwent greater numbers of surgeries (P P = 0.06), proliferative vitreoretinopathy (PVR) (P = 0.09), surgical approach (PPV and/or SB, P = 0.21), and tamponade type (P = 0.10) were not statistically significant, although they all achieved significance on univariate analysis (P = 0.001 or less). Intraoperative retinectomy (P = 0.009) and postoperative pseudophakia or aphakia (P = 0.008) were more frequent in the CME group, even after adjustment. Characteristics of cCME on OCT included diffuse distribution, confluent cysts, and absence of subretinal fluid or intraretinal hyperreflective foci. Macular thickness improved significantly with intravitreal triamcinolone (P = 0.016), but not with anti-vascular endothelial growth factor agents (P = 0.828) or dexamethasone implant (P = 0.125). After adjusting for number of surgeries and macular detachment, final visual acuities remained significantly lower in the CME vs nCME group (P = 0.012). Conclusion Risk factors of CME include complex retinal detachment repairs requiring multiple surgeries, and pseudophakic or aphakic lens status. Although this cCME was associated with poor therapeutic response, corticosteroids were the most effective studied treatments.

Dilated cardiomyopathy (DCM) is often associated with sarcomere protein mutations that confer reduced myofilament tension–generating capacity. We demonstrated that cardiac twitch tension-time integrals can be targeted and tuned to prevent DCM remodeling in hearts with contractile dysfunction. We employed a transgenic murine model of DCM caused by the D230N-tropomyosin (Tm) mutation and designed a sarcomere-based intervention specifically targeting the twitch tension-time integral of D230N-Tm hearts using multiscale computational models of intramolecular and intermolecular interactions in the thin filament and cell-level contractile simulations. Our models predicted that increasing the calcium sensitivity of thin filament activation using the cardiac troponin C (cTnC) variant L48Q can sufficiently augment twitch tension-time integrals of D230N-Tm hearts. Indeed, cardiac muscle isolated from double-transgenic hearts expressing D230N-Tm and L48Q cTnC had increased calcium sensitivity of tension development and increased twitch tension-time integrals compared with preparations from hearts with D230N-Tm alone. Longitudinal echocardiographic measurements revealed that DTG hearts retained normal cardiac morphology and function, whereas D230N-Tm hearts developed progressive DCM. We present a computational and experimental framework for targeting molecular mechanisms governing the twitch tension of cardiomyopathic hearts to counteract putative mechanical drivers of adverse remodeling and open possibilities for tension-based treatments of genetic cardiomyopathies., Tuning the molecular mechanisms that govern the twitch tension of cardiomyopathic hearts counteracts mechanical drivers of adverse remodeling.