Number Of Intramolecular Hydrogen Bonds Research Articles

Studying the ssDNA loaded adeno-associated virus aggregation using coarse-grained molecular dynamics simulations

The aggregation of adeno-associated viral (AAV) capsids in an aqueous environment was investigated via coarse-grained molecular dynamics (CG-MD) simulations. The primary driving force and mechanism of the aggregation were investigated with or without single-strand DNA (ssDNA) loaded at various process temperatures. Capsid aggregation appeared to involve multiple residue interactions (i.e., hydrophobic, polar and charged residues) leading to complex protein aggregation. In addition, two aggregation mechanisms (i.e., the fivefold face-to-face contact and the edge-to-edge contact) were identified from this study. The ssDNA with its asymmetric structure could be the reason for destabilizing protein subunits and enhancing the interaction between the charged residues, and further result in the non-reversible face-to-face contact. At higher temperature, the capsid structure was found to be unstable with the significant size expansion of the loaded ssDNA which could be attributed to reduced number of intramolecular hydrogen bonds, the increased conformational deviations of protein subunits and the higher residue fluctuations. The CG-MD model was further validated with previous experimental and simulation data, including the full capsid size measurement and the capsid internal pressure. Thus, a good understanding of AAV capsid aggregation, instability and the role of ssDNA were revealed by applying the developed computational model.

Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders.

TDP-43, an essential RNA/DNA-binding protein, is central to the pathology of neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia. Pathological mislocalization and aggregation of TDP-43 disrupt RNA splicing, mRNA stability, and mRNA transport, thereby impairing neuronal function and survival. The formation of amyloid-like TDP-43 filaments is largely facilitated by the destabilization of an α-helical segment within the disordered C-terminal region. In this study, we hypothesized that preventing the destabilization of the α-helical domain could potentially halt the growth of these pathological filaments. To explore this, we utilized a range of in silico techniques to design and evaluate peptide-based therapeutics that bind to pathological TDP-43 amyloid-like filament crystal structures and resist β sheet conversion. Our computational approaches, including biophysical and secondary structure property prediction, molecular docking, 3D structure prediction, and molecular dynamics simulations, were used to assess the structure, stability, and binding affinity of these peptides in relation to pathological TDP-43 filaments. The results of our in silico analyses identified a selection of promising peptides which displayed a stable α-helical structure, exhibited an increased number of intramolecular hydrogen bonds within the helical domain, and demonstrated high binding affinities for pathological TDP-43 amyloid-like filaments. Molecular dynamics simulations provided further support for the structural and thermodynamic stability of these peptides, as they exhibited lower root-mean-square deviation and more favorable free energy landscapes over 300 ns. These findings establish α-helical propensity peptides as potential lead molecules for the development of novel therapeutics against TDP-43 aggregation. This structure-based computational approach for the rational design of peptide inhibitors opens a new direction in the search for effective interventions for ALS, FTD, and other related neurodegenerative diseases. The peptides identified as the most promising candidates in this study are currently subject to further testing and validation through both in vitro and in vivo experiments.

Molecular Dynamics of Lysine Dendrigrafts in Methanol–Water Mixtures

The molecular dynamics method was used to study the structure and properties of dendrigrafts of the first and second generations in methanol-water mixtures with various volume fractions of methanol. At a small volume fraction of methanol, the size and other properties of both dendrigrafts are very similar to those in pure water. A decrease in the dielectric constant of the mixed solvent with an increase in the methanol fraction leads to the penetration of counterions into the dendrigrafts and a reduction of the effective charge. This leads to a gradual collapse of dendrigrafts: a decrease in their size, and an increase in the internal density and the number of intramolecular hydrogen bonds inside them. At the same time, the number of solvent molecules inside the dendrigraft and the number of hydrogen bonds between the dendrigraft and the solvent decrease. At small fractions of methanol in the mixture, the dominant secondary structure in both dendrigrafts is an elongated polyproline II (PPII) helix. At intermediate volume fractions of methanol, the proportion of the PPII helix decreases, while the proportion of another elongated β-sheet secondary structure gradually increases. However, at a high fraction of methanol, the proportion of compact α-helix conformations begins to increase, while the proportion of both elongated conformations decreases.

Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader

Chameleonicity (the capacity of a molecule to adapt its conformations to the environment) may help to identify orally bioavailable drugs in the beyond-Rule-of-5 chemical space. Computational methods to predict the chameleonic behaviour of degraders have not yet been reported and the identification of molecular chameleons still relies on experimental evidence. Therefore, there is a need to tune predictions with experimental data. Here, we employ PROTAC-1 (a passively cell-permeable degrader), for which NMR and physicochemical data prove the chameleonic behaviour, to benchmark the capacity of two conformational sampling algorithms and selection schemes. To characterize the conformational ensembles in both polar and nonpolar environments, we compute three molecular properties proven to be essential for cell permeability: conformer shape (radius of gyration), polarity (3D PSA), and the number of intramolecular hydrogen bonds. Energetic criteria were also considered. Infographics monitored the simultaneous variation of those properties in computed and NMR conformers. Overall, we provide key points for tuning conformational sampling tools to reproduce PROTAC-1 chameleonicity according to NMR evidence. This study is expected to improve the design of PROTAC drugs and the development of computational sustainable strategies to exploit the potential of new modalities in drug discovery.

Synthesis and Crystal Structure of Adamantylated 4,5,6,7-Tetrahalogeno-1H-benzimidazoles Novel Multi-Target Ligands (Potential CK2, M2 and SARS-CoV-2 Inhibitors); X-ray/DFT/QTAIM/Hirshfeld Surfaces/Molecular Docking Study

A series of new congeners, 1-[2-(1-adamantyl)ethyl]-1H-benzimidazole (AB) and 1-[2-(1-adamantyl)ethyl]-4,5,6,7-tetrahalogeno-1H-benzimidazole (Hal=Cl, Br, I; tClAB, tBrAB, tIAB), have been synthesized and studied. These novel multi-target ligands combine a benzimidazole ring known to show antitumor activity and an adamantyl moiety showing anti-influenza activity. Their crystal structures were determined by X-ray, while intermolecular interactions were studied using topological Bader's Quantum Theory of Atoms in Molecules, Hirshfeld Surfaces, CLP and PIXEL approaches. The newly synthesized compounds crystallize within two different space groups, P-1 (AB and tIAB) and P21/c (tClAB and tBrAB). A number of intramolecular hydrogen bonds, C-H⋯Hal (Hal=Cl, Br, I), were found in all halogen-containing congeners studied, but the intermolecular C-H⋯N hydrogen bond was detected only in AB and tIAB, while C-Hal⋯π only in tClAB and tBrAB. The interplay between C-H⋯N and C-H⋯Hal hydrogen bonds and a shift from the strong (C-H⋯Cl) to the very weak (C-H⋯I) attractive interactions upon Hal exchange, supplemented with Hal⋯Hal overlapping, determines the differences in the symmetry of crystalline packing and is crucial from the biological point of view. The hypothesis about the potential dual inhibitor role of the newly synthesized congeners was verified using molecular docking and the congeners were found to be pharmaceutically attractive as Human Casein Kinase 2, CK2, inhibitors, Membrane Matrix 2 Protein, M2, blockers and Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, inhibitors. The addition of adamantyl moiety seems to broaden and modify the therapeutic indices of the 4,5,6,7-tetrahalogeno-1H-benzimidazoles.

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 β, α+β, and α/β), 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.

Elucidating the mutational impact in causing Niemann–Pick disease type C: an in silico approach

Niemann–Pick disease type C is a rare autosomal recessive of lysosomal storage disorder characterized by impaired intracellular lipid transport and has a tendency to accumulate the fatty acids and glycosphingolipids in a variety of neurovisceral tissues. This work includes computational tools to deciphere the mutational effect in NPC protein. The study initiated with the collection of 471 missense mutations from various databases, which were then analyzed using computational tools. The mutations (G549V, F703S, Q775P and L1244P) were said to be disease associated, altering the biophysical properties, in highly conserved regions and reduces the stability using several in silico methods and were subjected to molecular docking analysis. To analyze the ligand (Itraconazole: a small molecule of antifungal drug class, which is known to inhibit cholesterol export from lysosomes) activity Molecular docking study was performed for all the complex proteins. The average binding affinity was taken and found to be −10.76 kcal/mol (native) and −11.06 kcal/mol (Q775P was located in transmembrane region IV which impacts the sterol-sensing domain of the NPC1 protein and associated with a severe infantile neurological form). Finally, molecular dynamic simulation was performed in duplicate and trajectories were built for the backbone of the RMSD, RMSF, the number of intramolecular hydrogen bonds, the radius of gyration and the SSE percent for both the complex proteins. This work contributes to understand the effectiveness and may provide an insight on the stability of the drug with the complex variant structures. Communicated by Ramaswamy H. Sarma

Inhibition of Inducible Nitric Oxide Synthase (iNOS) by Andrographolide and In Vitro Evaluation of Its Antiproliferative and Proapoptotic Effects on Cervical Cancer.

This work is aimed at investigating the expression levels of inducible nitric oxide synthase (iNOS) in cervical cancer and identifying a potential iNOS inhibitor. The data mining studies performed advocated iNOS to be a promising biomarker for cancer prognosis, as it is highly overexpressed in several malignant cancers. The elevated iNOS was found to be associated with poor survival and increased tumor aggressiveness in cervical cancer. Immunohistochemical and RT-PCR investigations of iNOS showed significant upregulation of endogenous iNOS expression in the cervical tumor samples, thus making iNOS a potent target for decreasing tumor inflammation and aggressiveness. Andrographolide, a plant-derived diterpenoid lactone, is widely reported to be effective against infections and inflammation, causing no adverse side effects on humans. In the current study, we investigated the effect of andrographolide on the prognostic value of iNOS expression in cervical cancer, which has not been reported previously. The binding efficacy of andrographolide was analyzed by performing molecular docking and molecular dynamic simulations. Multiple parameters were used to analyze the simulation trajectory, like root mean square deviation (RMSD), torsional degree of freedom, protein-root mean square fluctuations (P-RMSF), ligand RMSF, total number of intramolecular hydrogen bonds, secondary structure elements (SSE) of the protein, and protein complex with the time-dependent functions of MDS. Ligand-protein interactions revealed binding efficacy of andrographolide with tryptophan amino acid of iNOS protein. Cancer cell proliferation, cell migration, cell cycle analysis, and apoptosis-mediated cell death were assessed in vitro, post iNOS inhibition induced by andrographolide treatment (demonstrated by Western blot). Results. Andrographolide exhibited cytotoxicity by inhibiting the in vitro proliferation of cervical cancer cells and also abrogated the cancer cell migration. A significant increase in apoptosis was observed with increasing andrographolide concentration, and it also induced cell cycle arrest at G1-S phase transition. Our results substantiate that andrographolide significantly inhibits iNOS expression and exhibits antiproliferative and proapoptotic effects on cervical cancer cells.

Molecular Dynamics Simulation to Uncover the Mechanisms of Protein Instability During Freezing.

Freezing is a common process applied in the pharmaceutical industry to store and transport biotherapeutics. Herewith, multi-scale molecular dynamics simulations of Lactate dehydrogenase (LDH) protein in phosphate buffer with/without ice formation performed to uncover the still poorly understood mechanisms and molecular details of protein destabilization upon freezing. Both fast and slow ice growing conditions were simulated at 243K from one or two-side of the simulation box, respectively. The rate of ice formation at all-atom simulations was crucial to LDH stability, as faster freezing rates resulted in enhanced structural stability maintained by a higher number of intramolecular hydrogen bonds, less flexible protein's residues, lower solvent accessibility and greater structural compactness. Further, protein aggregation investigated by coarse-grained simulations was verified to be initiated by extended protein structures and retained by electrostatic interactions of the salt bridges between charged residues and hydrogen bonds between polar residues of the protein. Lastly, the study of free energy of dissociation through steered molecular dynamics simulation revealed LDH was destabilized by the solvation of the hydrophobic core and the loss of hydrophobic interactions. For the first time, experimentally validated molecular simulations revealed the detailed mechanisms of LDH destabilization upon ice formation and cryoconcentration of solutes.

Comparative analysis of the viscoelastic properties of collagen-like proteins by virtual creep test

Viscoelasticity of collagen is essential for the integrity of connective tissue and its aberrancy may result in collagen dysfunction and the emergence of connective tissue diseases. Precise identification of viscoelastic properties of collagens, and affecting factors are necessary to understand collagen behavior in the extracellular matrix as well as the mechanism of collagen-related diseases. The aim of this study is to investigate the mechanical and viscoelastic properties and time-lapse changes of protein-protein and protein-solvent hydrogen bonds of proline-rich and hydroxyproline-rich collagens by molecular dynamics simulation applying a virtual creep test. To this end, ten different collagen-like protein structures including [(Gly-Pro-Ala)7]3, [(Gly-Pro-Arg)7]3, [(Gly-Pro-Asp)7]3, [(Gly-Pro-Lys)7]3, [(Gly-Pro-Ser)7]3, [(Gly-Pro-Hyp)7]3, [(Gly-Ala-Hyp)7]3, [(Gly-Glu-Hyp)7]3, [(Gly-Leu-Hyp)7]3 and [(Gly-Val-Hyp)7]3 were virtually built and the viscoelastic properties of the structures were determined by virtual creep test according to Kelvin–Voigt model with various constant pulling forces. Different pulling forces ranged from 500 piconewton (pN) to 5000 pN were applied. As a result, Young’s modulus of the collagens was found positively correlated with the pulling force. The viscosity values and relaxation times were negatively correlated. Results also revealed a decreased number of intramolecular hydrogen bonds in hydroxyproline-rich collagens (but not in proline-rich collagens) and an increased number of protein-solvent hydrogen bonds in response to the increasing pulling force. Our results also confirmed that proline and hydroxyproline are the most critical amino acids in determining the collagen viscoelasticity. We suggest that collagen length and mechanical force may be additional important factors for biomechanical properties and behavior of collagen in the extracellular matrix. Communicated by Ramaswamy H. Sarma

Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe’s disease

Krabbe disease (KD), also known as globoid cell leukodystrophy disease, is an autosomal recessive lysosomal storage genetic disorder, which is caused by the deficiency of galactocerebrosidase (GALC) coding gene (GALC). This study aimed to use extensive computational pipelines in understanding the missense mutations in GALC. We retrieved 176 mutations from the public databases and subjected them to pathogenicity, stability, and conservation analyses. The PredictSNP, iStable, and ConSurf prediction tools predicted 45, 95, and 47 mutations to be deleterious, destabilizing, and highly conserved, respectively. The R396L and R396W were the most deleterious and destabilizing to GALC, and were therefore prioritized for further analysis. Systematic validation on the impact of the R396L and R396W mutations to the chaperone alpha lobeline was performed using the molecular docking approach. The docking analysis revealed that the mutant R396W interacted with minimal binding affinity compared with both the R396L mutant and native GALC. Furthermore, the repetitive molecular dynamics simulation analysis showed that the mutant R396W demonstrated less compactness and reduced number of intramolecular hydrogen bonds compared with the mutant R396L and the native GALC. Overall, we observed higher structural and functional modifications in R396W positioned in the substrate-binding site. This was highly supported by the MMPBSA and DSSP analysis of the GROMACS. DSSP showed the transformation of turns to bends, indicating a loss of stability due to the R396W mutation. This study is expected to serve as a platform for prioritizing mutant proteins that could be a platform for both drug and target therapeutics Communicated by Ramaswamy H. Sarma

In-silico study of single-strand DNA aptamers against cortisol as a potential biomarker receptor in therapeutics and diagnostics

Stress hormone is the number one adversary to the general health in human all over the world. In the presence of stress, cortisol, a glucocorticoid hormone synthesized by the stimulation of adrenal cortex will be secreted. Cortisol has immunosuppressive and anti-inflammatory effects, increases heart rate and blood pressure, and represses growth, and digestive and reproductive activities. Aptamers are synthetically derived nucleic acids has been long studied as a substitute of antibodies for therapeutics and diagnostics purposes. Current study focuses on in-silico approach of molecular docking and molecular dynamics simulation to study the interactions between single-strand DNA aptamers and cortisol in comparisons with the glucocorticoid receptor. In silico study were known to solve a plethora of biological related target study including the latest on COVID19 polymerase which is the inhibitors target protein. In current study, the tertiary conformational structures of ten single-strand DNA aptamers which experimentally derived were designed and docked against cortisol and compared with the binding of glucocorticoid receptor (PDB:4P6X). Binding affinity, number of hydrogen bonds and hydrophobic interactions were analyzed. The aptamer-cortisol complex with the lowest binding energy value was selected for 50 ns (ns) molecular dynamics simulation. Docking result shows that although number of intra-molecular hydrogen bond formed affecting the binding energy value of aptamer-cortisol complexes, hydrophobic interaction surrounding the cortisol is more important in determining the affinity of cortisol towards its receptor. Aptamer-1 shows the lowest binding energy value formed against cortisol (-10.1 kcal/mol) in comparison with other aptamers. Molecular dynamics simulation of Aptamer-1-cortisol complex shows that RMSD of glucocorticoid receptor-cortisol is lower in comparison with Aptamer 1-cortisol, with higher number of intra-molecular hydrogen bonds. Although the stability of receptor-cortisol is higher compared to Aptamer-1 complex, MMPBSA value of the last 10 ns of MD simulation prove that Aptamer-1-cortisol complex has the stability up to 50 ns of simulation. Further study to improve the single strand DNA aptamer binding against cortisol should be considered.

Stabilization of backbone-circularized protein is attained by synergistic gains in enthalpy of folded structure and entropy of unfolded structure.

Backbone circularization is an effective technique for protein stabilization. Here, we investigated the effect of a connector, an engineered segment that connects two protein termini, on the conformational stability of previously designed circularized variants of granulocyte colony-stimulating factor (G-CSF). Heat tolerance and chemical denaturation analyses revealed that aggregation resistance and thermodynamic stability of the circularized variants were superior to those of linear G-CSF. Crystal structure and molecular dynamics (MD) simulation of the most thermodynamically stable variant (C166) revealed a high number of intramolecular hydrogen bonds in both the connector region and Helix D adjacent to the connector region in the folded structure. MD simulations and theoretical calculations involving different force fields indicated a reduction in the main chain entropy of C166 in the unfolded state and increase in the intramolecular hydrogen bond energy of C166 in the folded structure. Although backbone circularization is usually considered to alter chain entropy of the unfolded state, the data indicated that it could also improve the conformational enthalpy of the folded state. Further structural examination of the connector region confirmed that protein design based on a statistical analysis of local structures is an effective approach for predicting an optimum connector length to improve the conformational stability of backbone-circularized proteins. Protein design using backbone circularization with an optimum connector length will be useful for the development of effective and safe protein therapeutics. DATABASE: Structural data are available in Protein Data Bank under the accession number 5ZO6.

Highly Selective and Sensitive Turn-Off-On Fluorescent Probes for Sensing Al3+ Ions Designed by Regulating the Excited-State Intramolecular Proton Transfer Process in Metal-Organic Frameworks.

The concept of high-performance excited-state intramolecular proton transfer (ESIPT)-based fluorescent metal-organic framework (MOF) probes for Al3+ is proposed in this work. By regulating the hydroxyl groups on the organic linker step by step, new fluorescent magnesium-organic framework (Mg-MOF) probes for Al3+ ions were established based on the ESIPT fluorescence mechanism. It is observed for the first time that the number of intramolecular hydrogen bonds between adjacent hydroxyl and carboxyl groups can effectively adjust the ESIPT process and lead to tunable fluorescence sensing performance. Together with the well-designed porous and anionic framework, the Mg-TPP-DHBDC probe decorating with a pair of intramolecular hydrogen bonds exhibits extra-high quantitative fluorescence response to Al3+ through an unusual turn-off (0-1.2 μM) and turn-on (4.2-15 μM) luminescence sensing mechanism. Notably, the 28 nM limit of detection value represents the lowest record among all reported MOF-based Al3+ fluorescent sensors up to now. Benefited from the unique turn-off-on ESIPT fluorescence detection process, the Mg-TPP-DHBDC MOF sensor exhibits single Al3+ detection compared with other 16 common metal ions including Ga3+, In3+, Fe3+, Cr3+, Ca2+, and Mg2+. Impressively, such an Al3+ selective sensing process can even be fulfilled by the reusable MOF test paper detected by naked eyes. Overall, the quantitative Al3+ detection, together with the extraordinary sensitivity, selectivity, fast response, and good reusability, strongly supports our concept of ESIPT-based fluorescent MOF Al3+ probes and makes Mg-TPP-DHBDC one of the most powerful Al3+ fluorescent sensors.

Analyses based on statistical thermodynamics for large difference between thermophilic rhodopsin and xanthorhodopsin in terms of thermostability.

Although the two membrane proteins, thermophilic rhodopsin (TR) and xanthorhodopsin (XR), share a high similarity in amino-acid sequence and an almost indistinguishable three-dimensional structure, TR is much more thermostable than XR. This is counterintuitive also because TR possesses only a smaller number of intramolecular hydrogen bonds (HBs) than XR. Here we investigate physical origins of the remarkable difference between XR and TR in the stability. Our free-energy function (FEF) is improved so that not only the portion within the transmembrane (TM) region but also the extracellular and intracellular portions within the water-immersed (WI) regions can be considered in assessing the stability. The assessment is performed on the basis of the FEF change upon protein folding, which is calculated for the crystal structure of XR or TR. Since the energetics within the TM region is substantially different from that within the WI regions, we determine the TM and WI portions of XR or TR by analyzing the distribution of water molecules using all-atom molecular dynamics simulations. The energetic component of the FEF change consists of a decrease in energy arising from the formation of intramolecular HBs and an increase in energy caused by the break of protein-water HBs referred to as "energetic dehydration penalty." The entropic component is a gain of the translational, configurational entropies of hydrocarbon groups within the lipid bilayer and of water molecules. The entropic component is calculated using the integral equation theory combined with our morphometric approach. The energetic one is estimated by a simple but physically reasonable method. We show that TR is much more stable than XR for the following reasons: The decrease in energy within the TM region is larger, and the energetic dehydration penalty within the WI regions is smaller, leading to higher energetic stabilization, and tighter packing of side chains accompanying the association of seven helices confers higher entropic stabilization on TR.

Elucidating the role of interacting residues of the MSH2-MSH6 complex in DNA repair mechanism: A computational approach.

The DNA repair system is crucial to repair the error resulting in DNA replication. MSH2-MSH6 protein complex plays a significant role in maintaining the mismatch repair mechanism. Mutations in the interface between the two proteins compromise their function in the repair process. The present study aims to understand the impact of missense mutations in the interacting sites of the MSH2-MSH6 protein complex. MSH6 is unstable due to the disordered N-terminal domain. This is stabilized by the MSH2 hetero-dimerization. We used pathogenicity and stability predictors to identify the missense mutations that could be more pathogenic with the destabilizing property. The mutations W764C of MSH2, and L1201F and G1316E of MSH6 were predicted to be highly deleterious and destabilizing by all the in silico predictors. The dynamic motion of the native and mutant (W764C) MSH2-MSH6 protein complexes was further investigated using Molecular Dynamics Simulations of the GROMACS package. The Root Mean Square Deviation (RMSD), Radius of Gyration (Rg), and change in a number of intramolecular hydrogen bonds (H-bonds) were analyzed using the embedded packages of GROMACS. From the simulation studies, we observed higher deviation, lower protein compactness, and a decrease in the number of intramolecular hydrogen bonds in the mutant W764C MSH2-MSH6 protein complex. The observed results from the computational methods suggest the involvement of higher structural impact on the MSH2-MSH6 protein complex upon W764C mutation could affect the DNA repair mechanism.

Effect of Familial Mutations on the Interconversion of α-Helix to β-Sheet Structures in an Amyloid-Forming Peptide: Insight from Umbrella Sampling Simulations.

Understanding the initial events of aggregation of amyloid β monomers to form β-sheet rich fibrils is useful for the development of therapeutics for Alzheimer's disease. In this context, the changes in energetics involved in the aggregation of helical amyloid β monomers into β-sheet rich dimers have been investigated using umbrella sampling simulations and density functional theory calculations. The results from umbrella sampling simulations for the free energy profile for the interconversion closely agree with the results of density functional theory calculations. The results reveal that helical peptides converted to β-sheet structures through coil-like conformations as intermediates that are mostly stabilized by intramolecular hydrogen bonds. The stabilization of intermediate structures could be a possible way to inhibit fibril formation. Mutations substantially decrease the height of the energy barrier for interconversion from α-helix to β-sheet structure when compared to that of the wild type, something that is attributed to an increase in the number of intramolecular hydrogen bonds between backbone atoms in the coil structures that correspond to a maximum value on the free energy surface. The reduction of the energy barrier leads to an enhancement of the rate of aggregation of amyloid β monomers upon introduction of various familial mutations, which is consistent with previous experimental reports.

Estimating the saturation vapor pressures of isoprene oxidation products C<sub>5</sub>H<sub>12</sub>O<sub>6</sub> and C<sub>5</sub>H<sub>10</sub>O<sub>6</sub> using COSMO-RS

Abstract. We have used COSMO-RS (the conductor-like screening model for real solvents), as implemented in the COSMOtherm program, to compute the saturation vapor pressures at 298 K of two photo-oxidation products of isoprene: the dihydroxy dihydroperoxide C5H12O6, and the dihydroperoxy hydroxy aldehyde, C5H10O6. The predicted saturation vapor pressures were significantly higher (by up to a factor of 1000) than recent experimental results, very likely due to the overestimation of the effects of intramolecular hydrogen bonds, which tend to increase saturation vapor pressures by stabilizing molecules in the gas phase relative to the liquid. Modifying the hydrogen bond enthalpy parameter used by COSMOtherm can improve the agreement with experimental results – however the optimal parameter value is likely to be system-specific. Alternatively, vapor pressure predictions can be substantially improved (to within a factor of 5 of the experimental values for the two systems studied here) by selecting only conformers with a minimum number of intramolecular hydrogen bonds. The computed saturation vapor pressures were very sensitive to the details of the conformational sampling approach, with the default scheme implemented in the COSMOconf program proving insufficient for the task, for example by predicting significant differences between enantiomers, which should have identical physical properties. Even after exhaustive conformational sampling, COSMOtherm predicts significant differences in saturation vapor pressures between both structural isomers and diastereomers. For C5H12O6, predicted differences in psat between structural isomers are up to 2 orders of magnitude, and differences between stereoisomers are up to a factor of 20 – though these differences are very likely exaggerated by the overestimation of the effect of intramolecular H-bonds. For C5H10O6, the maximum predicted differences between the three studied structural isomers and their diastereomer pairs are around a factor of 8 and a factor of 2, respectively, when only conformers lacking intramolecular hydrogen bonds are included in the calculations. In future studies of saturation vapor pressures of polyfunctional atmospheric oxidation products using COSMOtherm, we recommend first performing thorough conformational sampling and subsequently selecting conformers with a minimal number of intramolecular H-bonds.

Potentially helical imidazole-containing conjugated oligomers: synthesis, optical properties, and conformation

Three imidazole-containing conjugated oligomers (O1, O2, and O3) were synthesized by a Suzuki–Miyaura cross-coupling polymerization in combination with a post-polymerization reaction to clarify the structure–property–conformation relationship and ultimately develop a method for accessing helical secondary structures in the future. HR-ESI-MS analysis of the model reaction mixture revealed that debromination is responsible for the low molecular weight of these oligomers. The absorption and emission peak maxima gradually redshifted moving from O2 to O1 to O3, which can be rationalized by the number of intramolecular hydrogen bonds (IHBs). O2, with no IHBs, and O3, which forms multiple robust IHBs, were insensitive to the nature of the solvent, while O1, with weak IHBs, exhibited solvent-dependent absorption spectra. O3 was susceptible to both acid and base treatment, namely, the addition of HCl caused a blueshift in the absorption spectra, and the addition of NaOH resulted in a complex shift in the peak depending on the degree of deprotonation. A conformational study based on DFT calculations indicated that the formation of the IHB network potentially endows O3 with a helical conformation. The formation of multiple intramolecular hydrogen bonds (IHBs) is a reliable method for obtaining conjugated oligomers with helical secondary structures, and imidazole with both proton-accepting and proton-donating abilities plays an important role. On the basis of its optical properties in conjunction with DFT calculations, a conjugated oligomer composed of alternating imidazole and 1,4-dihydroxybenzene units was found to (1) form robust IHBs, (2) be susceptible to both acid and base treatment, and (3) potentially adopt a helical conformation.

Computational approach to unravel the impact of missense mutations of proteins (D2HGDH and IDH2) causing D-2-hydroxyglutaric aciduria 2.

The 2-hydroxyglutaric aciduria (2-HGA) is a rare neurometabolic disorder that leads to the development of brain damage. It is classified into three categories: D-2-HGA, L-2-HGA, and combined D,L-2-HGA. The D-2-HGA includes two subtypes: type I and type II caused by the mutations in D2HGDH and IDH2 proteins, respectively. In this study, we studied six mutations, four in the D2HGDH (I147S, D375Y, N439D, and V444A) and two in the IDH2 proteins (R140G, R140Q). We performed in silico analysis to investigate the pathogenicity and stability changes of the mutant proteins using pathogenicity (PANTHER, PhD-SNP, SIFT, SNAP, and META-SNP) and stability (i-Mutant, MUpro, and iStable) predictors. All the mutations of both D2HGDH and IDH2 proteins were predicted as disease causing except V444A, which was predicted as neutral by SIFT. All the mutants were also predicted to be destabilizing the protein except the mutants D375Y and N439D. DSSP plugin of the PyMOL and Molecular Dynamics Simulations (MDS) were used to study the structural changes in the mutant proteins. In the case of D2HGDH protein, the mutations I147S and V444A that are positioned in the beta sheet region exhibited higher Root Mean Square Deviation (RMSD), decrease in compactness and number of intramolecular hydrogen bonds compared to the mutations N439D and D375Y that are positioned in the turn and loop region, respectively. While the mutants R140Q and R140QG that are positioned in the alpha helix region of the protein. MDS results revealed the mutation R140Q to be more destabilizing (higher RMSD values, decrease in compactness and number of intramolecular hydrogen bonds) compared to the mutation R140G of the IDH2 protein. This study is expected to serve as a platform for drug development against 2-HGA and pave the way for more accurate variant assessment and classification for patients with genetic diseases.