Identification of HOC•HC(O)H, HOCH2C•O, and HOCH2CH2O• Intermediates in the Reaction of H + Glycolaldehyde in Solid Para-Hydrogen and Its Implication to the Interstellar Formation of Complex Sugars.

Glycolaldehyde [HOCH2C(O)H, GA], the primitive sugar-like molecule detected in the interstellar medium (ISM), is a potential precursor for the synthesis of complex sugars. Despite its importance, the mechanism governing the formation of these higher-order sugars from GA under interstellar circumstances remains elusive. Radical intermediates HOCH2CH2O• (1), HOCH2C•HOH (2), HOCH2C•O (3), HOC•HC(O)H (4), and O•CH2C(O)H (5) derived from GA could be potential precursors for the formation of glyceraldehyde (aldose sugar), dihydroxyacetone (ketose sugar), and ethylene glycol (sugar alcohol) in dark regions of ISM. However, the spectral identification of these intermediates and their roles were little investigated. We conducted reactions involving H atoms and the Cis-cis conformer of GA (Cc-GA) in solid p-H2 at 3.2 K and identified IR spectra of radicals Cc-HOCH2C•O (3) and Cc-HOC•HC(O)H (4) produced from H abstraction as well as closed-shell HOCHCO (6) produced via consecutive H abstraction of GA. In addition, Cc-HOCH2CH2O• (1) and C•H2OH + H2CO (7) were produced through the H addition and the H-induced fragmentation channels, respectively. In darkness, when only H-tunneling reactions occurred, the formation of (3) was major and that of (1) was minor. In contrast, during IR irradiation to produce H atoms with higher energy, the formation of (4) and C•H2OH + H2CO (7) became important. We also successfully converted most Cc-GA to the second-lowest-energy conformer Trans-trans-GA (Tt-GA) by prolonged IR irradiation at 2827 nm to investigate H + Tt-GA; Tt-HOCH2C•O (3'), Tt-HOC•HC(O)H (4'), HOCHCO (6), Tt-HOCH2CH2O• (1'), and C•H2OH + H2CO (7) were observed. We discuss possible routes for the formation of higher-order sugars or related compounds involving (7), (1), (3), and (4), but neither (2), which was proposed previously, nor (5) plays a significant role in H + GA. Such previously unreported rich chemistry in the reaction of H + GA, with four channels of three distinct types, indicates the multiple roles that GA might play in astronomical chemistry.

Fundamental Aspects of Phase-Separated Biomolecular Condensates.

Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.

Recurrent Radiculopathy Following Transforaminal Lumbar Interbody Fusion: Successful Management with Endoscopic Sacroiliac Joint Ablation.

Introduction: Low back pain persisting after spine surgery presents diagnostic and treatment complexities for spine surgeons. Failed back syndrome is a term usually used to characterize chronic back or leg pain following spine surgery. Research has indicated a range of persistent pain occurrences after spine surgery. The sacroiliac joint (SIJ) has been recognized as a potential source of pain for a long time but has not received sufficient attention in subsequent years. Dysfunctions in the SIJ can result in a spectrum of clinical conditions, such as low back pain and lower limb radiculopathy. Traditional treatment approaches for SIJ disorders often involve conservative measures such as physical therapy, medications, intra-articular injections, and surgical options. In the past decade, endoscopic SIJ ablation has emerged as a minimally invasive alternative for managing SIJ pain and dysfunction. This approach combines minimal invasiveness with precise targeting, potentially reducing morbidity and enabling quicker recovery compared to open surgical procedures. Case Report: A 60-year-old female patient with grade 2 L5-S1 lytic listhesis initially underwent lumbar interbody fusion to address chronic low back pain and radiculopathy, resulting in significant symptom resolution for a brief period. The patient experienced a resurgence of symptoms within a short duration that proved refractory to conventional medical management and interventional pain management procedures. Ultimately, the patient achieved sustained relief after undergoing endoscopic SIJ ablation. Conclusion: This case report highlights the importance of endoscopic SIJ ablation as an innovative treatment for recurrent lower limb radiculopathy. Focusing on the SIJ, often neglected in lumbar spine surgery, this minimally invasive procedure shows promise in alleviating symptoms and enhancing patient outcomes.

Amino Acid-Dependent Material Properties of Tetrapeptide Condensates.

Condensates formed by intrinsically disordered proteins mediate a myriad of cellular processes and are linked to pathological conditions including neurodegeneration. Rules of how different types of amino acids (e.g., π-π pairs) dictate the physical properties of biomolecular condensates are emerging, but our understanding of the roles of different amino acids is far from complete. Here we studied condensates formed by tetrapeptides of the form XXssXX, where X is an amino acid and ss represents a disulfide bond along the backbone. Eight peptides form four types of condensates at different concentrations and pH values: droplets (X = F, L, M, P, V, A); amorphous dense liquids (X = L, M, P, V, A); amorphous aggregates (X = W), and gels (X = I, V, A). The peptides exhibit enormous differences in phase equilibrium and material properties, including a 368-fold range in the threshold concentration for phase separation and a 3856-fold range in viscosity. All-atom molecular dynamics simulations provide physical explanations of these results. The present work also reveals widespread critical behaviors, including critical slowing down manifested by the formation of amorphous dense liquids and critical scaling obeyed by fusion speed, with broad implications for condensate function.

Adenosine Triphosphate Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks.

Adenosine triphosphate (ATP) is an abundant molecule with crucial cellular roles as the energy currency and a building block of nucleic acids and for protein phosphorylation. Here we show that ATP mediates the phase separation of basic intrinsically disordered proteins (bIDPs). In the resulting condensates, ATP is highly concentrated (apparent partition coefficients up to 7700) and serves as bridges between bIDP chains. These liquid-like droplets have some of the lowest interfacial tension (∼25 pN/µm) but high zero-shear viscosities (1-15 Pa s) due to the bridged protein networks, and yet their fusion has some of the highest speeds (∼1 µm/ms). The rapid fusion manifests extreme shear thinning, where the apparent viscosity is lower than zero-shear viscosity by over 100-fold, made possible by fast reformation of the ATP bridges. At still higher concentrations, ATP does not dissolve bIDP droplets but results in aggregates and fibrils.

Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein.

The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. At debate is its oligomeric state, let alone its function. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein was previously found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identify only a front-to-front, symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.

A common pathway for detergent-assisted oligomerization of Aß42.

Amyloid beta (Aß) aggregation is a slow process without seeding or assisted nucleation. Sodium dodecyl sulfate (SDS) micelles stabilize Aß42 small oligomers (in the dimer to tetramer range); subsequent SDS removal leads to a 150-kD Aß42 oligomer. Dodecylphosphorylcholine (DPC) micelles also stabilize an Aß42 tetramer. Here we investigate the detergent-assisted oligomerization pathway by solid-state NMR spectroscopy and molecular dynamics simulations. SDS- and DPC-induced oligomers have the same structure, implying a common oligomerization pathway. An antiparallel ß-sheet formed by the C-terminal region, the only stable structure in SDS and DPC micelles, is directly incorporated into the 150-kD oligomer. Three Gly residues (at positions 33, 37, and 38) create holes that are filled by the SDS and DPC hydrocarbon tails, thereby turning a potentially destabilizing feature into a stabilizing factor. These observations have implications for endogenous Aß aggregation at cellular interfaces.

ATP Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks.

ATP is an abundant molecule with crucial cellular roles as the energy currency and a building block of nucleic acids and for protein phosphorylation. Here we show that ATP mediates the phase separation of basic intrinsically disordered proteins (bIDPs). In the resulting condensates, ATP is highly concentrated (apparent partition coefficients at 200-5000) and serves as bridges between bIDP chains. These liquid-like droplets have some of the lowest interfacial tension (~25 pN/µm) but high zero-shear viscosities (1-15 Pa s) due to the bridged protein networks, and yet their fusion has some of the highest speeds (~1 µm/ms). The rapid fusion manifests extreme shear thinning, where the apparent viscosity is lower than zero-shear viscosity by over 100-fold, made possible by fast reformation of the ATP bridges. At still higher concentrations, ATP does not dissolve bIDP droplets but results in aggregates and fibrils.

Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein.

The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein has been found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identified only a symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.

Infrared spectra of isoquinolinium (iso-C9H7NH+) and isoquinolinyl radicals (iso-C9H7NH and 1-, 3-, 4-, 5-, 6-, 7- and 8-iso-HC9H7N) isolated in solid para-hydrogen.

Protonated polycyclic aromatic nitrogen heterocycles (H+PANH) are prospective candidates that may contribute to interstellar unidentified infrared (UIR) emission bands because protonation enhances the relative intensities of the bands near 6.2, 7.7 and 8.6 µm, and the presence of the N atom induces a blue shift of the ring-stretching modes so that the spectra of H+PANH match better with the 6.2 µm feature in class-A UIR spectra. We report the infrared (IR) spectra of protonated isoquinoline (the 2-isoquinolinium cation, iso-C9H7NH+), its neutral counterpart (the 2-isoquinolinyl radical, iso-C9H7NH), and another mono-hydrogenated product (the 6-isoquinolinyl radical, 6-iso-HC9H7N), produced on the electron-bombardment of a mixture of isoquinoline (iso-C9H7N) with excess para-hydrogen (p-H2) during matrix deposition at 3.2 K. To generate additional isomers of hydrogenated isoquinoline, we irradiated iso-C9H7N/Cl2/p-H2 matrices at 365 nm to generate Cl atoms, followed by IR irradiation to generate H atoms via Cl + H2 (v = 1) → HCl + H; the H atoms thus generated reacted with iso-C9H7N. In addition to iso-C9H7NH and 6-iso-HC9H7N observed in the electron-bombardment experiments, we identified six additional hydrogenated isoquinoline species, 1-, 3-, 4-, 5-, 7- and 8-iso-HC9H7N, via their IR spectra; hydrogenation on the N atom and all available carbon atoms except for the two sharing carbon atoms on the fused ring was observed. Spectral groupings were achieved according to their behaviors after maintenance of the matrix in darkness and on secondary photolysis at various wavelengths. The assignments were supported via comparison of the experimental results with the vibrational wavenumbers and IR intensities of possible isomers predicted using the B3LYP/6-311++G(d,p) method. The implications in the identification of the UIR band are discussed.

Two gates mediate NMDA receptor activity and are under subunit-specific regulation.

Kinetics of NMDA receptor (NMDAR) ion channel opening and closing contribute to their unique role in synaptic signaling. Agonist binding generates free energy to open a canonical gate at the M3 helix bundle crossing. Single channel activity is characterized by clusters, or periods of rapid opening and closing, that are separated by long silent periods. A conserved glycine in the outer most transmembrane helices, the M4 helices, regulates NMDAR function. Here we find that the GluN1 glycine mainly regulates single channel events within a cluster, whereas the GluN2 glycine mainly regulates entry and exit from clusters. Molecular dynamics simulations suggest that, whereas the GluN2 M4 (along with GluN2 pre-M1) regulates the gate at the M3 helix bundle crossing, the GluN1 glycine regulates a 'gate' at the M2 loop. Subsequent functional experiments support this interpretation. Thus, the distinct kinetics of NMDARs are mediated by two gates that are under subunit-specific regulation.

Spectral Evidence of Bevel-Gear-Type Rotation of Benzene around Br in Solid p-H2: Infrared Spectrum of the C6H6Br Radical.

Whether the structure of C6H6X (X = halogen), an intermediate in the halogenation of benzene, is an open or a bridged form has been debated. We produced Br to react with C6H6 upon photolysis in situ of a Br2/C6H6/p-H2 matrix at 3.2 K. In contrast to the C6H6Cl σ-complex reported previously, the observed infrared spectrum indicates that C6H6Br is an open-form π-complex. Furthermore, lines of the two CH out-of-plane bending modes associated mainly with even- and odd-numbered carbons, predicted near 672 and 719 cm-1, merged into a broad line at 697.3 cm-1, indicating that these modes become nearly equivalent as Br migrates from one carbon atom to another. Quantum-chemical calculations support that the benzene ring performs a bevel-gear-type rotation with respect to Br. Observation of only trans-ortho- and trans-para-C6H6Br2 suggests that this gear-type motion allows the additional Br atom to attack C6H6Br only from the opposite side of the Br atom in C6H6Br.

SpiDec: Computing binodals and interfacial tension of biomolecular condensates from simulations of spinodal decomposition.

Phase separation of intrinsically disordered proteins (IDPs) is a phenomenon associated with many essential cellular processes, but a robust method to compute the binodal from molecular dynamics simulations of IDPs modeled at the all-atom level in explicit solvent is still elusive, due to the difficulty in preparing a suitable initial dense configuration and in achieving phase equilibration. Here we present SpiDec as such a method, based on spontaneous phase separation via spinodal decomposition that produces a dense slab when the system is initiated at a homogeneous, low density. After illustrating the method on four model systems, we apply SpiDec to a tetrapeptide modeled at the all-atom level and solvated in TIP3P water. The concentrations in the dense and dilute phases agree qualitatively with experimental results and point to binodals as a sensitive property for force-field parameterization. SpiDec may prove useful for the accurate determination of the phase equilibrium of IDPs.

ReSMAP: Web Server for Predicting Residue-Specific Membrane-Association Propensities of Intrinsically Disordered Proteins.

The functional processes of many proteins involve the association of their intrinsically disordered regions (IDRs) with acidic membranes. We have identified the membrane-association characteristics of IDRs using extensive molecular dynamics (MD) simulations and validated them with NMR spectroscopy. These studies have led to not only deep insight into functional mechanisms of IDRs but also to intimate knowledge regarding the sequence determinants of membrane-association propensities. Here we turned this knowledge into a web server called ReSMAP, for predicting the residue-specific membrane-association propensities from IDR sequences. The membrane-association propensities are calculated from a sequence-based partition function, trained on the MD simulation results of seven IDRs. Robustness of the prediction is demonstrated by leaving one IDR out of the training set. We anticipate there will be many applications for the ReSMAP web server, including rapid screening of IDR sequences for membrane association.

A chemical link between methylamine and methylene imine and implications for interstellar glycine formation.

Methylamine CH3NH2 is considered to be an important precursor of interstellar amino acid because hydrogen abstraction might lead to the aminomethyl radical •CH2NH2 that can react with •HOCO to form glycine, but direct evidence of the formation and spectral identification of •CH2NH2 remains unreported. We performed the reaction H + CH3NH2 in solid p-H2 at 3.2 K and observed IR spectra of •CH2NH2 and CH2NH upon irradiation and when the matrix was maintained in darkness. Previously unidentified IR spectrum of •CH2NH2 clearly indicates that •CH2NH2 can be formed from the reaction H + CH3NH2 in dark interstellar clouds. The observed dual-cycle mechanism containing two consecutive H-abstraction and two H-addition steps chemically connects CH3NH2 and CH2NH in interstellar media and explains their quasi-equilibrium. Experiments on CD3NH2 produced CD2HNH2, in addition to •CD2NH2 and CD2NH, confirming the occurrence of H addition to •CD2NH2.

Assessments of right ventricular strain using cardiac magnetic resonance imaging following kidney transplantation.

Although kidney transplantation (KT) has been shown to ameliorate adverse left ventricular (LV) remodelling associated with end stage kidney disease, its effects on the right ventricle have not been well studied. Recently, strain imaging has been shown to be a sensitive measure of early subclinical myocardial dysfunction. Using cardiac magnetic resonance imaging (MRI), we examined the effects of KT on right ventricular (RV) strain parameters. In a cohort of 81 patients (39 patients underwent KT and 42 patients remained on dialysis as control group), cardiac MRI studies were obtained at baseline and at 1 year follow-up. There were no significant differences in RV strain values between the groups at baseline. After 1 year, RV strain values did not significantly change in patients who received KT, and changes in RV strain over 1 year were not significantly different between the KT and the dialysis groups. Given the previously demonstrated improvement in LV strain post-KT, the current study suggests that RV and LV remodelling post-KT may have different mechanisms. Further studies elucidating the effects of KT on RV remodelling are needed.

Molecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19. The Sulfonamides groups have been widely introduced in several drugs, especially for their antibacterial activities and generally prescribed for respiratory infections. On the other hand, imidazole groups have the multipotency to act as drugs, including antiviral activity. We have used a structure-based drug design approach to design some imidazole derivatives of sulfonamide, which can efficiently bind to the active site of SARS-CoV-2 main protease and thus may have the potential to inhibit its proteases activity. We conducted molecular docking and molecular dynamics simulation to observe the stability and flexibility of inhibitor complexes. We have checked ADMET (absorption, distribution, metabolism, excretion and toxicity) and drug-likeness rules to scrutinize toxicity and then designed the most potent compound based on computational chemistry. Our small predicted molecule non-peptide protease inhibitors could provide a useful model in the further search for novel compounds since it has many advantages over peptidic drugs, like lower side effects, toxicity and less chance of drug resistance. Further, we confirmed the stability of our inhibitor-complex and interaction profile through the Molecular dynamics simulation study. Our small predicted moleculeCommunicated by Ramaswamy H. Sarma.

Non-energetic, Low-Temperature Formation of Cα-Glycyl Radical, a Potential Interstellar Precursor of Natural Amino Acids.

The reaction of H atoms with glycine was investigated at 3.1 K in para-H2, a quantum-solid host. The reaction was followed by IR spectroscopy, with the spectral analysis aided by quantum chemical computations. Comparison of the experimental IR spectrum with computed anharmonic frequencies and intensities proved that, regardless of the reactant glycine conformation, Cα-glycyl radical is formed in an H-atom-abstraction process with great selectivity. The product of the second H-atom abstraction, iminoacetic acid, was also observed in a smaller amount. The Cα-glycyl radical is sensitive to UV light and decomposes to iminoacetic acid and H atom upon 280 nm radiation. Since the reactive radical center is located on the Cα-atom, it is suggested that natural α-amino acids can be formed from glycine via the Cα-glycyl radical by non-energetic mechanisms in the solid phase of the interstellar medium.

Vitamin D Levels and the Risk of Posttransplant Diabetes Mellitus After Kidney Transplantation.

INTRODUCTION: Given the burden of posttransplant diabetes mellitus and the high prevalence of low vitamin D levels in kidney transplant recipients, it is reasonable to consider vitamin D as a novel and potentially modifiable risk factor in this patient population. RESEARCH QUESTION: To determine the association between 25- hydroxyvitamin D (25(OH)D) level and posttransplant diabetes among kidney transplant recipients. Design: In a multi-center cohort study of 442 patients who received a kidney transplant between January 1, 2005 and December 31, 2010, serum samples within one-year before transplant were analyzed for 25(OH)D levels. The association between 25(OH)D and posttransplant diabetes were examined in Cox proportional hazard models. RESULTS: The median 25(OH)D level was 66 nmol/L. The cumulative probability of diabetes at 12-months by quartiles of 25(OH)D (< 42, 42 to 64.9, 65 to 94.9, and > 95 nmol/L) were 23.4%, 26.9%, 21.4%, and 15.6%, respectively. Compared to the highest 25(OH)D quartile, hazard ratios (95% CI) for the risk were 1.85 (1.03, 3.32), 2.01 (1.12, 3.60), 1.77 (0.96, 3.25) across the first to third quartiles, respectively. The associations were accentuated in a model restricted to patients on tacrolimus. When modeled as a continuous variable, 25(OH)D levels were significantly associated with a higher risk of diabetes (hazard ratio 1.06, 95% CI: 1.01, 1.13 per 10 nmol/L decrease). DISCUSSION: Serum 25(OH)D was an independent predictor of posttransplant diabetes in kidney transplant recipients. These results may inform the design of trials using vitamin D to reduce the risk in kidney transplant recipients.

Membrane Association and Functional Mechanism of Synaptotagmin-1 in Triggering Vesicle Fusion.

Upon Ca2+ influx, synaptic vesicles fuse with the presynaptic plasma membrane (PM) to release neurotransmitters. Membrane fusion is triggered by synaptotagmin-1, a transmembrane protein in the vesicle membrane (VM), but the mechanism is under debate. Synaptotagmin-1 contains a single transmembrane helix (TM) and two tandem C2 domains (C2A and C2B). This study aimed to use molecular dynamics simulations to elucidate how Ca2+-bound synaptotagmin-1, by simultaneously associating with VM and PM, brings them together for fusion. Although C2A stably associates with VM via two Ca2+-binding loops, C2B has a propensity to partially dissociate. Importantly, an acidic motif in the TM-C2A linker competes with VM for interacting with C2B, thereby flipping its orientation to face PM. Subsequently, C2B readily associates with PM via a polybasic cluster and a Ca2+-binding loop. The resulting mechanistic model for the triggering of membrane fusion by synaptotagmin-1 reconciles many experimental observations.