Accurate Prediction of Antifreeze Protein from Sequences through Natural Language Text Processing and Interpretable Machine Learning Approaches.

Antifreeze proteins (AFPs) bind to growing iceplanes owing to their structural complementarity nature, thereby inhibiting the ice-crystal growth by thermal hysteresis. Classification of AFPs from sequence is a difficult task due to their low sequence similarity, and therefore, the usual sequence similarity algorithms, like Blast and PSI-Blast, are not efficient. Here, a method combining n-gram feature vectors and machine learning models to accelerate the identification of potential AFPs from sequences is proposed. All these n-gram features are extracted from the K-mer counting method. The comparative analysis reveals that, among different machine learning models, Xgboost outperforms others in predicting AFPs from sequence when penta-mers are used as a feature vector. When tested on an independent dataset, our method performed better compared to other existing ones with sensitivity of 97.50%, recall of 98.30%, and f1 score of 99.10%. Further, we used the SHAP method, which provides important insight into the functional activity of AFPs.

Supramolecular alternating copolymers with highly efficient fluorescence resonance energy transfer.

This article reports alternating supramolecular copolymerization of two naphthalene-diimide (NDI)-derived building blocks (NDI-1 and NDI-2) under thermodynamic control. Both monomers contain a central NDI chromophore, attached to a hydrocarbon-chain and a carboxylic-acid group. The NDI core in NDI-2 is symmetrically substituted with two butane-thiol groups, which makes it distinct from NDI-1. In decane, a 1 : 1 mixture of NDI-1 and NDI-2 shows spontaneous gelation and a typical fibrillar network, unlike the behavior of either of the components individually. The solvent-dependent UV/vis spectrum of the mixed sample in decane shows bathochromically shifted sharp absorption bands and a sharp emission band (holds a mirror-image relationship) with a significantly small Stokes shift compared to those in CHCl3, indicating J-aggregation. In contrast, the aggregated spectra of the individual monomers show broad structureless features, suggesting ill-defined aggregates. Cooling curves derived from the temperature-dependent UV/vis spectroscopy studies revealed early nucleation and a signature of well-defined cooperative polymerization for the mixed sample, unlike either of the individual components. Molecular dynamics simulations predicted the greatest dimer formation tendency for the NDI-1 + NDI-2 (1 : 1), followed by pure NDI-1 and NDI-2. Theoretical studies further revealed a partial positive charge in the NDI ring of NDI-1 when compared to NDI-2, promoting the alternating stacking propensity, which is also favored by the steric factor as NDI-2 is core-substituted with alkyl thiols. Such theoretical predictions fully corroborate with the experimental results showing 1 : 1 stoichiometry (from Job's plot) of the two monomers, indicating alternate stacking sequences in the H-bonded (syn-syn catemer type) supramolecular copolymer. Such alternating supramolecular copolymers showed highly efficient (>93%) fluorescence resonance energy transfer (FRET).

Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid-Liquid Phase Separation.

Liquid-liquid phase separation (LLPS) by disordered proteins has been shown to govern biological processes and cause numerous diseases. Therefore, a deeper understanding of the interactions and their variation with external factors is key to modulating the LLPS behavior of different systems and protecting proteins from pathological aggregation. In this context, we have looked at interactions between similarly charged peptides to understand the molecular features that may drive or prevent condensate formation under various conditions. We have studied dimer formation for model peptides where charged and noncharged amino acids have been placed alternatively. Using arginine and glutamic acid as the charged residues and varying the other residues with glycine, alanine, and proline to alter hydrophobicity, we have obtained the free-energy surface (FES) for the dimer formation for these systems under high salt concentration at two different temperatures using all-atom molecular dynamics simulations and the well-tempered metadynamics method. Our results indicate that a combination of effects such as hydrophobicity, arginine-arginine interactions, or water release from the solvation shell makes dimerization free energy more favorable for the positively charged peptides with lower flexibility. For the negatively charged peptides, the crucial role of water has been found in governing the FES. Systems having charged residues and phenylalanine in the peptide sequence also have been studied at high salt concentrations using unbiased simulations. In this case, only the positively charged peptides were found to aggregate through temperature-dependent hydrophobic and cation-π interactions. Overall, our study indicates that the negatively charged peptides are more likely to remain in the dilute phase under various conditions compared to the positively charged systems. The findings from our study would be helpful in designing and controlling systems to obtain LLPS behavior for therapeutic usage.

Preferential Ordering and Organization of Hydration Water Favor Nucleation of Ice by Ice-Nucleating Proteins over Antifreeze Proteins.

Bacteria containing ice-nucleating proteins (INPs) evolved in nature to nucleate ice at the high sub-zero ambiance. The ability of the INPs to induce order in the hydration layer and their aggregation propensity appear to be key factors of their ice nucleation abilities. However, the mechanism of the process of ice nucleation by INPs is yet to be understood clearly. Here, we have performed all-atom molecular dynamics simulations and analyzed the structure and dynamics of the hydration layer around the proposed ice-nucleating surface of a model INP. Results are compared with the hydration of a topologically similar non-ice-binding protein (non-IBP) and another ice-growth inhibitory antifreeze protein (sbwAFP). We observed that the hydration structure around the ice-nucleating surface of INP is highly ordered and the dynamics of the hydration water are slower, compared to the non-IBP. Even the ordering of the hydration layer is more evident around the ice-binding surface of INP, compared to the antifreeze protein sbwAFP. Particularly with increasing repeat units of INP, we observe an increased population of ice-like water. Interestingly, the distances between the hydroxyl groups of the threonine ladder and its associated channel water of the ice-binding surface (IBS) of INP in the X and Y direction mimic the oxygen atom distances of the basal plane of hexagonal ice. However, the structural synergies between the hydroxyl group distances of the threonine ladder and its associated channel water of the IBS of sbwAFP and oxygen atom distances of the basal plane are less evident. This difference makes the IBS of the INP a better template for ice nucleation than AFP, although both of them bind to the ice surface efficiently.

Real-time Observation of Macroscopic Helical Morphologies under Optical Microscope: A Curious Case of π-π Stacking Driven Molecular Self-assembly of an Organic Gelator Devoid of Hydrogen Bonding.

Supramolecular assemblies such as tubules/helix/double helix/helical tape etc. are usually submicron objects preventing direct observation under optical microscope. Chiral-pure form of these assemblies is important for potential applications. Herein, we report a rare phenomenon wherein a DMSO gel of a simple terpyridine derivative [(4-CNPhe)4PyTerp] produced macroscopic helical morphologies (µm length scale) which could be observed under optical microscope, formation of which could be monitored by optical videography, stable enough to withstand acidic vapour, robust enough to display reversible gel↔sol in response to acidic and ammonia vapour and sturdy enough to be maneuvered with a needle. These properties appeared to be unique to the title compound as the other related derivatives failed to display such assembly structures. SXRD and MD simulation studies suggested that weak interactions (π-π stacking) played a crucial role in the self-assembly process.

Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control.

Kinesin motor proteins perform several essential cellular functions powered by the adenosine triphosphate (ATP) hydrolysis reaction. Several single-point mutations in the kinesin motor protein KIF5A have been implicated to hereditary spastic paraplegia disease (HSP), a lethal neurodegenerative disease in humans. In earlier studies, we have shown that a series of HSP-related mutations can impair the kinesin's long-distance displacement or processivity by modulating the order-disorder transition of the linker connecting the heads to the coiled coil. On the other hand, the reduction of kinesin's ATP hydrolysis reaction rate by a distal asparagine-to-serine mutation is also known to cause HSP disease. However, the molecular mechanism of the ATP hydrolysis reaction in kinesin by this distal mutation is still not fully understood. Using classical molecular dynamics simulations combined with quantum mechanics/molecular mechanics calculations, the pre-organization geometry required for optimal hydrolysis in kinesin motor bound to α/ß-tubulin is determined. This optimal geometry has only a single salt-bridge (of the possible two) between Arg203-Glu236, putting a reactive water molecule at a perfect position for hydrolysis. Such geometry is also needed to create the appropriate configuration for proton translocation during ATP hydrolysis. The distal asparagine-to-serine mutation is found to disrupt this optimal geometry. Therefore, the current study along with our previous one demonstrates how two different effects on kinesin dynamics (processivity and ATP hydrolysis), caused by a different set of genotypes, can give rise to the same phenotype leading to HSP disease.

Number of Hydrogen Bonds per Unit Solvent Accessible Surface Area: A Descriptor of Functional States of Proteins.

Proteins function close to native and near-native conformations. These states are evolutionarily selected to ensure the effect of mutations is minimized. The structural organization of a protein is hierarchical and modular, which reduces the dimensionality of the configurational space of the native states. Thus, finding appropriate descriptors that define the native state among all possible states of a protein is a problem of immense interest. The present study explores the correlation between solvent accessible surface areas (SASAs) and different intraprotein as well as protein-water hydrogen bonds of 55 single-chain globular proteins from four different structural classes (all α, all ß, α+ß, and α/ß), 16 multichain proteins, and 4 macromolecular complexes. A systematic analysis of the solvent accessible surface area and intraprotein and protein-water hydrogen bonds suggests a linear relationship between SASAs and hydrogen bonds. The number of protein-water hydrogen bonds per unit SASA ranges from 3 to 4 for all the different structural protein classes. In contrast, the number of intramolecular hydrogen bonds per unit SASA, including the mainchain-mainchain, mainchain-sidechain, and sidechain-sidechain, varies between 0.75 to 2. The solvation free energy of a protein linearly decreases with SASA. Our study also shows that the solvation free energy/SASA varies from -75 to -105 kJ mol-1 nm-2 across all the native states studied here. The number conservancy of intraprotein hydrogen bonds per unit SASA possibly imparts structural stability to the native structure. On the other hand, 3-4 protein-water hydrogen bonds per unit SASA are possibly required to maintain a balance between the solubility and functionality of the native states. This study provides a basis for synthetic biologists to design new folds with improved functionality.

Molecular Factors of Ice Growth Inhibition for Hyperactive and Globular Antifreeze Proteins: Insights from Molecular Dynamics Simulation.

The molecular mechanism behind the ice growth inhibition by antifreeze proteins (AFPs) is yet to be understood completely. Also, what physical parameters differentiate between the AFP and non-AFP are largely unknown. Thus, to get an atomistic overview of the differential antifreeze activities of different classes of AFPs, we have studied ice growth from different ice surfaces in the presence of a moderately active globular type III AFP and a hyperactive spruce budworm (sbw) AFP. Results are compared with the observations of ice growth simulations in the presence of topologically similar non-AFPs using all-atom molecular dynamics simulations. Simulation data suggest that the ice surface coverage is a critical factor in ice growth inhibition. Due to the presence of an ice binding surface (IBS), AFPs form a high affinity complex with ice, accompanied by a transition of hydration water around the IBS from clathrate-like to ice-like. Several residues around the periphery of the IBS anchor the AFP to the curved ice surface mediated by multiple strong hydrogen bonds, stabilizing the complex immensely. In the high surface coverage regime, the slow unbinding kinetics dominates over the ice growth kinetics and thus facilitates the ice growth inhibition. Due to the non-availability of a proper IBS, non-AFPs form a low-affinity complex with the growing ice surface. As a result, the non-AFPs are continuously repelled by the surface. If the concentration of AFPs is low, then the effective surface coverage is reduced significantly. In this low surface coverage regime, AFPs can also behave like impurities and are engulfed by the growing ice crystal.

Identifying the Template for Oligomer to Fibril Conversion for Amyloid-ß (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics.

The toxicity of amyloid-ß (Aß) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aß aggregates. In this study, we investigate Aß13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aß13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel ß-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the ß-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aß42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.

Direct Participation of Solvent Molecules in the Formation of Supramolecular Polymers.

This article reports supramolecular polymerization of two bis-amide functionalized naphthalene-diimide (NDI) building blocks (NDI-L and NDI-C) in two solvents, namely n-heptane (Hep) and methylcyclohexane (MCH). NDI-L and NDI-C differ only by the peripheral hydrocarbon wedges, consisting of linear C7 chains or cyclic methylcyclohexane rings, respectively. UV/Vis and FTIR spectroscopy studies reveal distinct internal order and H-bonding pattern for NDI-L and NDI-C aggregates irrespective of the solvent system, indicating the dominant role of the intrinsic packing parameters of the individual building block, possibly influenced by the peripheral steric crowding. However, NDI-L produces a significantly stronger gel in Hep compared to MCH as evident from the rheological and thermal properties. In contrast, NDI-C exhibits a clear preference for MCH, producing gel with moderate strength but in Hep it fails to produce 1D morphology or gelation. All-atom molecular dynamics (MD) simulation studies corroborate with the experimental observation and provide the rationale for the observed solvent-shape effect by revealing a quantitative estimate regarding the thermodynamics of self-assembly in these four combinations. Such clear-cut shape-matching effect (between the peripheral hydrocarbon wedge and the solvent system) unambiguously support a direct participation of the solvent molecules during supramolecular polymerization and presence of a closely-adhered solvent shell around the supramolecular polymers, similar to the first layer of water molecules around the protein surface. Solvent induced CD experiments support this hypothesis as induced CD band was observed only from a chiral co-solvent of matching shape. This is reconfirmed by the higher de-solvation temperature of the shape-matching NDI/solvent system combination compared to the shape mis-match combination in variable temperature UV/Vis experiments, revealing transformation to a different aggregate at higher temperatures rather than disassembly to the monomer for all four combinations.

Curious Case of MAD2 Protein: Diverse Folding Intermediates Leading to Alternate Native States.

Anfinsen's dogma postulates that for one sequence there will be only one unique structure that is necessary for the functioning of the protein. However, over the years there have been a number of departures from this postulate. As far as function is considered, there are growing examples of proteins that "moonlight", perform multiple unrelated functions. With the discovery of intrinsically disordered proteins, morpheeins, chameleonic sequences, and metamorphic proteins that can switch folds, we have acquired a more nuanced understanding of protein folding and dynamics. Appearing to apparently contradict the classical folding paradigm, metamorphic proteins are considered exotic species. In this work, we have explored the free energy landscape and folding pathways of the metamorphic protein MAD2 which is an important component of the spindle checkpoint. It coexists in two alternate states: the inactive open state and the active closed state. Using a dual-basin structure-based model approach we have shown that a variety of intermediates and multiple pathways are available to MAD2 to fold into its alternate forms. This approach involves performing molecular dynamics simulations of coarse-grained models of MAD2 where the structural information regarding both of its native conformations is explicitly included in terms of their native contacts in the force field used. Detailed analyses have indicated that some of the contacts within the protein play a key role in determining which folding pathway will be selected and point to a probable long-range communication between the N and the C termini of the protein that seems to control its folding. Finally, our work also provides a rationale for the experimentally observed preference of the ΔC10 variant of MAD2 to exist in the open state.

Molecular Insight into the Effect of a Single-Nucleotide Polymorphic Variation on the Structure and Dynamics of Methionine Synthase Reductase and Its Association with Neural Tube Defects.

Neural tube defects (NTDs) are among the common and severe congenital malformations in neonates. According to a WHO report, nearly three lakh babies are affected per year worldwide by NTDs. Most studies revealed that folate deficiency is the key element to promote NTD with other oligogenic and multifactorial elements. This folate is metabolized by the FOCM (folate one-carbon metabolism) pathway. The most important step in the FOCM pathway is the conversion of methionine to homocysteine, which is guided by the enzyme MTRR. Several single-nucleotide polymorphisms (SNPs) in the MTRR gene are strongly associated with the progression of NTD. A nonsynonymous allelic variant (rs1532268) of the protein leads to a missense mutation at the 202nd position from serine to leucine (S202L) and is associated with a higher disease prevalence in different populations. In our study, this SNP indicates a 2-fold increase in the risk of disease progression (p-value of 0.03; OR 2.76; 95% CI 1.08-7.11). Here, extensive molecular dynamics simulations and interaction network analysis reveal that the change of 202nd serine to leucine alters the structures of the FAD and NAD binding domains, which restricts the ligand binding. The S202L variation alters the functional dynamics that might impede the electron transport chain along the NADP(H)→ FAD→ FMN pathway and hamper phosphorylation by kinases like GSK-3 and CaM-II during the posttranscriptional modification of the protein. The present study provides functional insights into the effect of the genetic variations of the MTRR gene on the NTD disease pathogenesis.

Kinetic and thermodynamic stability comparison for the fibrillar form of small amyloid-ß(1-42) oligomers using scaled molecular dynamics.

Amyloid-ß (Aß) oligomers act as intermediates for several neurodegenerative disease-relevant fibril formations. However, gaining insight into the oligomer to fibril conversion process remains a challenge due to the transient nature of small Aß. In this study, we probe the kinetic and thermodynamic stabilities of small Aß(1-42) oligomers in fibrillar conformations to understand from what size these aggregates start forming stable fibrils. With no definite structures available for small Aß42 aggregates, we have started with oligomers extracted from mature fibrils having four, five, six and nine chains stacked together, and have performed order-to-disorder transition on these systems. Using scaled molecular dynamics (sMD) simulation, the timescale for breaking the native contacts of fibrils has been compared. The results indicate that the kinetic stability of oligomers increases with size, especially at the C-terminus end beyond five-chain oligomers. The free energy of breaking the contacts at the ß-sheet regions in the structures has been obtained on an unscaled potential from a free energy extrapolation (FEE) approach. The values show that although stable minima are obtained for larger oligomers due to the enhanced stability of the C-terminus ends, fully stable fibril formation may require aggregates larger than the ones considered in our study. Additionally, dissimilar kinetics for the unbinding of terminal chains across all the oligomers has been observed. The interaction energy values calculated from unscaled MD simulations reveal the crucial role of water in our observations. Our work provides the application of an easy-to-deploy method that sheds light on interactions which could be significant in the early stages of Aß42 fibril formation.

Role of Calcium in Modulating the Conformational Landscape and Peptide Binding Induced Closing of Calmodulin.

Metal ions play an essential role in several cellular functions. Calcium is a ubiquitous regulator and is involved in numerous physiological processes. A class of proteins have evolved that sense calcium levels inside cells and act as effector molecules. Calmodulin is one such protein that gets activated after binding to calcium and thereafter interacts with its many targets. Calmodulin comprises two homologous domains that are connected by a flexible linker. The calcium-dependent flexibility of the linker results in numerous conformations of calmodulin. In this work using microsecond long MD simulations and well-tempered metadynamics, we explore how the calcium induced conformation dynamics of calmodulin is different from the inherent fluctuations of apocalmodulin and whether it has any role in preparing calmodulin for its interaction with its target-smooth muscle myosin light chain kinase (smMLCK). We have observed that calcium bound calmodulin could explore states that are predisposed toward peptide binding. We also found that though the binding of calmodulin to smMLCK peptide is calcium-independent, calcium regulates the domain to which the peptide will be bound. On the basis of our findings, we have proposed two alternate pathways for smMLCK peptide binding to calmodulin as directed by the ambient calcium concentrations. Our work proposes how calmodulin functions under physiologically dynamic calcium concentrations.

Mechanistic basis of propofol-induced disruption of kinesin processivity.

Propofol is a widely used general anesthetic to induce and maintain anesthesia, and its effects are thought to occur through impact on the ligand-gated channels including the GABAA receptor. Propofol also interacts with a large number of proteins including molecular motors and inhibits kinesin processivity, resulting in significant decrease in the run length for conventional kinesin-1 and kinesin-2. However, the molecular mechanism by which propofol achieves this outcome is not known. The structural transition in the kinesin neck-linker region is crucial for its processivity. In this study, we analyzed the effect of propofol and its fluorine derivative (fropofol) on the transition in the neck-linker region of kinesin. Propofol binds at two crucial surfaces in the leading head: one at the microtubule-binding interface and the other in the neck-linker region. We observed in both the cases the order-disorder transition of the neck-linker was disrupted and kinesin lost its signal for forward movement. In contrast, there was not an effect on the neck-linker transition with propofol binding at the trailing head. Free-energy calculations show that propofol at the microtubule-binding surface significantly reduces the microtubule-binding affinity of the kinesin head. While propofol makes pi-pi stacking and H-bond interactions with the propofol binding cavity, fropofol is unable to make a suitable interaction at this binding surface. Therefore, the binding affinity of fropofol is much lower compared to propofol. Hence, this study provides a mechanism by which propofol disrupts kinesin processivity and identifies transitions in the ATPase stepping cycle likely affected.

Computational modeling of dynein motor proteins at work.

Along with various experimental methods, a combination of theoretical and computational methods is essential to explore different length-scale and time-scale processes in the biological system. The functional mechanism of a dynein, an ATP-fueled motor protein, working in a multiprotein complex, involves a wide range of length/time-scale events. It generates mechanical force from chemical energy and moves on microtubules towards the minus end direction while performing a large number of biological processes including ciliary beating, intracellular material transport, and cell division. Like in the cases of other conventional motor proteins, a combination of experimental techniques including X-crystallography, cryo-electron microscopy, and single molecular assay have provided a wealth of information about the mechanochemical cycle of a dynein. Dyneins have a large and complex structural architecture and therefore, computational modeling of different aspects of a dynein is extremely challenging. As the process of dynein movement involves varying length and timescales, it demands, like in experiments, a combination of computational methods covering such a wide range of processes for the comprehensive investigation of the mechanochemical cycle. In this review article, we will summarize how the use of state-of-the-art computational methods can provide a detailed molecular understanding of the mechanochemical cycle of the dynein. We implemented all-atom molecular dynamics simulations and hybrid quantum-mechanics/molecular-mechanics simulations to explore the ATP hydrolysis mechanisms at the primary ATPase site (AAA1) of dynein. To investigate the large-scale conformational changes we employed coarse-grained structure-based molecular dynamics simulations to capture the domain motions. Here we explored the conformational changes upon binding of ATP at AAA1, nucleotide state-dependent regulation of the mechanochemical cycle, and inter-head coordination by inter-head tension. Additionally, implementing a phenomenological theoretical model we explore the force-dependent detachment rate of a motorhead from the microtubule and the principle of multi-dynein cooperation during cargo transport.

Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution.

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP-36) protein unfolds gradually in presence of water-ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman-Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local-bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.

Structural insight into the effect of polymorphic variation on the functional dynamics of methionine synthase reductase: Implications in neural tube defects.

Neural tube defects (NTDs), one of the most common birth defects, are strongly associated with the variations of several single nucleotide polymorphisms (SNPs) in the MTRR gene. The gene codes a key enzyme that is involved in the rejuvenation of methionine synthase activity. An allelic variant of the protein leads to missense mutation at 49th position from isoleucine to methionine (I49M) is associated with higher disease prevalence in different populations. Here, extensive molecular dynamics simulations and interaction network analysis reveal that the 49th isoleucine is a crucial residue that allosterically regulates the dynamics between the flavin mononucleotide (FMN) and NADP(H) binding domains. I49M variation alters the functional dynamics in a way that might impede the electron transport chain along the NADP(H) â†’ flavin adenine dinucleotide â†’ FMN pathway. The present study provides functional insights into the effect of the genetic variations of the MTRR gene on the NTDs disease pathogenesis.

On the Correlation between Pair Hydrophobicity and Mixing Enthalpies in Water-Alcohol Binary Mixtures.

In this article, we have explored the extent of pair hydrophobicity in water-alcohol binary mixtures upon varying the chain length of the alcohol at several compositions. We have measured the pair hydrophobicity in water-methanol, water-propanol, and water-butanol mixtures. The pair hydrophobicity is measured by the depth of the first minimum (contact minimum) in the potential of mean force profile between a pair of neopentanes. In the case of water-methanol mixtures, the pair hydrophobicity is highest at xMeOH = 0.25, whereas in water-propanol mixtures, it is highest at xPrOH = 0.07, and in water-butanol mixture pair, hydrophobicity is highest at even lower alcohol concentration (xBuOH = 0.03). This indicates that as we increase the chain length of alcohol, the composition at which pair hydrophobicity is highest shifts toward a lower alcohol composition of the binary mixture. We have shown that the composition dependence of pair hydrophobicity echoes the trend observed in the calculated composition dependence of the enthalpy of mixing of the alcohol-water binary mixtures. The association pattern of the hydrophobic part of the alcohol also shows a change in trend around similar alcohol compositions. The hydrogen bond pattern around the alcohol rather than water exhibits a change in trend around those compositions. These results will improve our understanding of the composition-dependent phenomena of biomolecular processes in aqueous binary mixtures.

Novel Mechanism of Cholesterol Transport by ABCA5 in Macrophages and Its Role in Dyslipidemia.

Cholesterol homeostasis results from a delicate interplay between influx and efflux of free cholesterol primarily mediated by ABCA1. Here we report downregulation of ABCA1 in hyper-cholesterol conditions in macrophages, which might be responsible for compromised reverse cholesterol transport and hyperlipidemia. Surprisingly, this is countered by the upregulation of a lesser known family member ABCA5 to maintain cholesterol efflux. The relative contribution of ABCA1 and ABCA5 toward cholesterol efflux was evaluated and revealed ABCA5 as the primary efflux mediator under high cholesterol load. These observations were correlated to cholesterol load in circulation in vivo, and we observed an inverse expression profile in mice models of atherosclerosis (ApoE-/-) and hyperlipidemia (PPARα-/-) in response to high cholesterol diet. Observations were further validated in human plasma samples. Simulation studies revealed a unique conformation of ABCA5 proposing a favored route for cholesterol loading onto high-density lipoproteins for reverse cholesterol transport. Thus, our study implicates a functional complementation between these two transporters, formulating an efficient strategy to maintain efflux in cholesterol excess conditions in macrophages.