Comparative Molecular Dynamics Simulations Research Articles

Interactions Between Antimicrobial Peptides and Targets Responsible for their Nephrotoxic Action: Molecular Dynamics Simulations.

Polymyxin is the last line of defense against resistant forms of microorganisms, but it has significant nephrotoxicity. One of the directions in reducing the nephrotoxicity of polymyxin is to modify the charge of the molecule and accordingly, to change the topicity of the polymyxin derivative to the renal megalin. Such modification can lead to a decrease in the accumulation of polymyxin in the kidneys and reduce its toxicity while maintaining its antimicrobial properties. The study aimed to investigate the structural aspects of polymyxin nephrotoxicity at the atomic level to promote the more purposeful development of the polymyxin's derivatives with the lower nephrotoxic action. The molecular dynamics simulations of the complexes of polymyxin B and its derivative NAB7061 (that carries only three positive charges located within the macrocycle) with megalin were performed in program package YASARA structure with explicit water (TIP3P) and ions (0.9 % NaCl) in NPT ensemble using the AMRER03 force field. After 10 ns equilibration, each system was simulated at 298 K and pH 7.4 for a 25 ns production phase. Simulations were run twice for each molecular system. By molecular dynamics simulations, the possibility was shown for polymyxin to form a stable complex with two neighbor structural domains of megalin in accord with the universal mechanism of binding the cationic ligands by ligand-binding CR repeats of the LDLR-family receptors. It was reported that interactions of megalin with polymyxin were stronger than with its derivative having no positively charged groups outside the macrocycle. The structural prerequisites of these differences were revealed, explaining the less nephrotoxicity of such derivatives compared to polymyxin. Comparative molecular dynamics simulations of megalin interactions with polymyxin B and its derivative NAB7061, which carries no positive charges outside the macrocycle, revealed the possible structural prerequisites for the lower nephrotoxic action of such polymyxin derivatives. The weakening of polymyxins binding with megalin may become an effective preventive measure against polymyxin-induced nephrotoxicity.

Comparative Molecular Dynamics Simulation of Wetting on Liquid-like Surfaces.

We utilize molecular dynamics simulations to comparably investigate the wetting and motion behavior of droplets on liquid-like surfaces (LLS) with varying grafting conditions. Polydimethylsiloxane (PDMS) and perfluoropolyether (PFPE) have been considered to be flexible molecules versus rigid molecules of trichloro(octadecyl) silane (OTS) and trichloro(1H,1H,2H,2H-perfluorooctyl) silane (PFOS), respectively. Our findings reveal that droplets on surfaces tethered with either PDMS or PFPE brushes can generate indentations and wetting ridges, providing microscopic evidence of their liquid-like nature. The grafting density of mobile chains exerts a dominant influence on the wetting properties compared to the molecular weight. A parameter map is created to pinpoint the precise range of grafting densities essential for the optimal construction of LLS at predetermined molecular weights. Furthermore, the investigation of droplet motion dynamics on LLS demonstrates that droplets consistently exhibit a rolling state, regardless of the intensity of the applied lateral force. The movement pattern of the droplet shifts only under conditions where the grafting density is significantly reduced and the substrate exhibits hydrophilic tendencies. These findings and the developed model are anticipated to offer valuable guidelines for optimal designs of LLS.

In-Silico study of Destabilizing Alzheimer’s Aβ42 Protofibrils with Curcumin.

Aggregation of amyloid beta (Aβ) peptides leads to formation of fibrilar, soluble oligomers, and their deposition is a key event in progression of Alzheimer’s disease (AD). Recent experimental studies of (Curcumin) showed\ significant Aβ aggregation inhibition, but its molecular mechanism is not yet clear. Hence, the present study aims at exploring the underlying mechanism of destabilization and inhibition of aggregation of the Aβ protofibril by Curcumin at the molecular level. Molecular docking analysis shows that Curcumin binds to chain E of the Aβ protofibril through hydrogen bonding interactions. Comparative molecular dynamics simulations depict the binding of Curcumin at the edge of chain E, and its partially inserted conformation at the hydrophobic core destabilizes the Aβ protofibril. Its binding causes loss of hydrophobic contacts, leading to a partial opening of tightly packed β-sheet protofibrils. The hydration effect of salt bridge between the amino group of Lys28 and the oxygen atom of Curcumin contributes in destabilization of Aβ protofibrils. Binding free energy calculations of Curcumin and the Aβ protofibril showed that van der Waals interactions are dominant over the others. Thus, our results revealed that Curcumin interacts mainly with the hydrophobic core along with positively charged residues of the Aβ protofibril for effective destabilization. Thus, this structural information could be useful to design new inhibitors to control the aggregation of Aβ protofibrils in AD patients.

Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family.

Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (Topt) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear. Here, we studied the cold-adaptation mechanisms of alginate lyases by comparing four members of the PL7 family from different environments: AlyC3 from the Arctic ocean (Psychromonas sp. C-3), AlyA1 from the temperate ocean (Zobellia galactanivorans), PA1167 from the human pathogen (Pseudomonas aeruginosa PAO1), and AlyQ from the tropic ocean (Persicobacter sp. CCB-QB2). Sequence comparison and comparative molecular dynamics (MD) simulations revealed two main strategies of cold adaptation. First, the Arctic AlyC3 and temperate AlyA1 increased the flexibility of the loops close to the catalytic center by introducing insertions at these loops. Second, the Arctic AlyC3 increased the electrostatic attractions with the negatively charged substrate by introducing a high portion of positively charged lysine at three of the insertions mentioned above. Furthermore, our study also revealed that the root mean square fluctuation (RMSF) increased greatly when the temperature was increased to Topt or higher, suggesting the RMSF increase temperature as a potential indicator of the cold adaptation level of the PL7 family. This study provided new insights into the cold-adaptation mechanisms of bacterial alginate lyases and the marine carbon cycling at low temperatures.

Mapping structural and dynamic divergence across the MBOAT family

Membrane-bound O-acyltransferases (MBOATs) are membrane-embedded enzymes that catalyze acyl chain transfer to a diverse group of substrates, including lipids, small molecules, and proteins. MBOATs share a conserved structural core, despite wide-ranging functional specificity across both prokaryotes and eukaryotes. The structural basis of catalytic specificity, regulation and interactions with the surrounding environment remain uncertain. Here, we combine comparative molecular dynamics (MD) simulations with bioinformatics to assess molecular and interactional divergence across the family. In simulations, MBOATs differentially distort the bilayer depending on their substrate type. Additionally, we identify lipid binding sites surrounding reactant gates in the surrounding membrane. Complementary bioinformatic analyses reveal a conserved role for re-entrant loop-2 in MBOAT fold stabilization and a key hydrogen bond bridging DGAT1 dimerization. Finally, we predict differences in MBOAT solvation and water gating properties. These data are pertinent to the design of MBOAT-specific inhibitors that encompass dynamic information within cellular mimetic environments.

Clues to the Design of Aggregation-Resistant Insulin from Proline Scanning of Highly Amyloidogenic Peptides Derived from the N-Terminal Segment of the A-Chain.

Insulin aggregation poses a significant problem in pharmacology and medicine as it occurs during prolonged storage of the hormone and in vivo at insulin injection sites. We have recently shown that dominant forces driving the self-assembly of insulin fibrils are likely to arise from intermolecular interactions involving the N-terminal segment of the A-chain (ACC1-13). Here, we study how proline substitutions within the pilot GIVEQ sequence of this fragment affect its propensity to aggregate in both neutral and acidic environments. In a reasonable agreement with in silico prediction based on the Cordax algorithm, proline substitutions at positions 3, 4, and 5 turn out to be very effective in preventing aggregation according to thioflavin T-fluorescence-based kinetic assay, infrared spectroscopy, and atomic force microscopy (AFM). Since the valine and glutamate side chains within this segment are strongly involved in the interactions with the insulin receptor, we have focused on the possible implications of the Q → P substitution for insulin's stability and interactions with the receptor. To this end, comparative molecular dynamics (MD) simulations of the Q5P mutant and wild-type insulin were carried out for both free and receptor-bound (site 1) monomers. The results point to a mild destabilization of the mutant vis à vis the wild-type monomer, as well as partial preservation of key contacts in the complex between Q5P insulin and the receptor. We discuss the implications of these findings in the context of the design of aggregation-resistant insulin analogues retaining hormonal activity.

Structure‐Based Approaches for the Prediction of Alzheimer's Disease Inhibitors: Comparative Interactions Analysis, Pharmacophore Modeling and Molecular Dynamics Simulations

AbstractDue to its significant role in neurodegeneration, Cyclin‐dependent kinase 5 (CDK5) has emerged as a potential target for addressing neuropathological disorders, including Alzheimer's disease (AD). The application of CDK5 inhibitors has demonstrated promise in the treatment of AD. This prompted us to model this interesting target using a computational workflow named Docking‐based Comparative Intermolecular Contacts Analysis (dbCICA). Approaches including 3D‐QSAR, genetic algorithm, and pharmacophore modeling were employed to discover new CDK inhibitors.

Biochemical and biophysical characterization of biosynthetic arginine decarboxylase from Thermus thermophilus

The biosynthetic arginine decarboxylase in Thermus thermophilus is responsible for producing spermidine, a polyamine with numerous biological applications in humans. The arginine decarboxylase has significant applications in biotechnology industries, suggesting the need to evaluate its biochemical and biophysical characteristics at the molecular level. In this study, both in vitro and in silico methods were employed to investigate the structural and functional behavior of the arginine decarboxylase protein. In in vitro, MALDI-TOF, size exclusion, and assay studies were performed to examine the nature and activity of the protein. The MALDI-TOF analysis confirmed the purified protein as biosynthetic arginine decarboxylase. The assay results revealed that the Pyridoxal 5’-Phosphate (PLP) cofactor plays a crucial role in enhancing enzyme activity by producing agmatine (a by-product of spermidine). Further, optimum enzyme activity was observed at 50 °C, suggesting the extremophilic nature of the enzyme. Unlike other proteins, this enzyme displayed optimal activity at both acidic and basic pH, demonstrating its sensitivity to pH changes. Furthermore, the addition of divalent ions like Mg 2+ increased the rate of reaction. In in silico, structure modeling, and comparative molecular dynamics simulation studies were used to assess the protein stability and behavior at different pH and temperature conditions. The findings of this study could be applied to improve enzyme production in the industry. Communicated by Ramaswamy H. Sarma

Comparative molecular dynamics simulation of apo and holo forms of the P53 mutant C176F: a structural perspective

Zinc fingers represent a highly diverse structural domain, with P53 being a notable example among zinc-dependent transcription factors. The folding patterns of proteins in the cell are heavily influenced by the concentration of zinc. The potential for zinc loss arises due to its dysregulation and the frequent occurrence of tumorigenic P53 mutations. This could lead to significant consequences such as protein misfolding and a reduction in tumor-suppressing capabilities. To gain deeper insights into the structural conformation, stability, flexibility, and compactness of the zinc-binding mutation C176F, a comprehensive comparative computational analysis was conducted on the wildtype (WT) and mutant (MT) P53 in the presence (Holo) and absence (Apo) of zinc. This analysis was performed using molecular dynamic simulation. The overall observation was that the mutation in C176F reduces the metal binding affinity and results in less stability in the Apo and Holo P53 MT protein.

Crystallographic mining driven computer-guided approach to identify the ASK1 inhibitor likely to perturb the catalytic region

The pathological levels of reactive oxygen species (ROS) and oxidative stress has been recognized as a critical driver for inflammatory disorders. Apoptosis signal-regulating kinase 1 (ASK1) has been reported to be activated by intracellular ROS and its inhibition leads to a down regulation of p38-and JNK-dependent signaling. ASK1 inhibitors are reported to have the potential to treat clinically important inflammatory pathologies including liver, pulmonary and renal disorders. In view of its biological and pathological significance, inhibition of ASK1 with small molecules has been pursued as an attractive strategy to combat human diseases such as non-alcoholic steatohepatitis (NASH). Despite several ASK1 inhibitors being developed, the failure in Phase 3 clinical trials of most advanced candidate selonsertib’s, underscores to discover therapeutic agents with diverse chemical moiety. Here, by using structural pharmacophore and enumeration strategy on mining co-crystals of ASK1, different scaffolds were generated to enhance the chemical diversity keeping the critical molecular interaction in the catalytic site intact. A total of 15,772 compounds were generated from diverse chemical scaffolds and were evaluated using a virtual screening pipeline. Based on docking and MM-GBSA scores, a lead candidate, S3C-1-D424 was identified from top hits. A comparative molecular dynamics simulations (MD) of APO, Selonsertib and shortlisted potential candidates combined with pharmacokinetics profiling and thermodynamic analysis, demonstrating their suitability as potential ASK1 inhibitors to explore further for establishment towards hit-to-lead campaign.Communicated by Ramaswamy H. Sarma

Light-induced enhanced phase change process of plasmonic nanofluids: The reduction of the latent heat of vaporization

Recently, some studies have shown that the light-induced localized surface plasmon resonance (LSPR) effect of plasmonic nanoparticles can significantly influence the gas–liquid phase change process of nanofluids, but the mechanism is still not clear. In this work, we conducted several comparative experiments and molecular dynamics (MD) simulations to investigate the reduction of the latent heat of vaporization (LHV) of plasmonic nanofluids (PNFs) under the impact of the LSPR effect. During the experiments, gold nanofluids with different concentrations were comparatively heated using a heat gun and monochromatic incident lights, and the LHV was calculated based on the Clausius-Clapeyron equation. It is found that when the LSPR effect is excited, the LHV of gold nanofluids with high concentrations can be dramatically reduced by 60.2 % under the combined effect of thermal diffusion and enhanced electric field (EEF). To further investigate the impact of the LSPR-induced EEF on the gas–liquid phase change process of PNFs, a modified MD simulation was used for calculating the LHV of gold nanofluids. The result reveals that nanoparticles not only act as ‘heat sources’ that transfer the thermal energy to the surrounding liquid when the LSPR effect is excited but also can excite the EEF to directly accelerate the motion of liquid molecules from the liquid state to the gaseous state. This work clearly reveals that the LSPR-induced EEF plays a crucial role in both the evaporation and boiling process of PNFs.

Computational insights into potential marine natural products as selective inhibitors of Mycobacterium tuberculosis InhA: A structure-based virtual screening study

Several factors are associated with the emergence of drug resistance mechanisms, such as impermeable cell walls, gene mutations, and drug efflux systems. Consequently, bacteria acquire resistance, leading to a decrease in drug efficacy. A new and innovative strategy is required to combat drug resistance in tuberculosis (TB) effectively. Therefore, targeting the mycolic acid biosynthesis pathway, which is involved in synthesising mycolic acids (MAs), essential structural components responsible for mycobacterial pathogenicity, has garnered interest in TB research and the concept of drug resistance. In this context, InhA, which plays a crucial role in the fatty acid synthase-II (FAS-II) system of the MA biosynthetic pathway, was selected as a druggable target for screening investigation. To identify potential lead molecules against InhA, diverse marine natural products (MNPs) were collected from the comprehensive marine natural products database (CMNPD). Virtual screening studies aided in selecting potential lead molecules that best fit within the substrate-binding pocket (SBP) of InhA, forming crucial hydrogen bond interaction with the catalytic residue Tyr158. Three MNPs, CMNPD30814, CMNPD1702, and CMNPD27355, were chosen as prospective alternative molecules due to their favorable pharmacokinetic properties and lack of toxicity according to ProTox-II predictions. Additionally, improved reactivity of the MNPs was observed in the results of density functional theory (DFT) studies. Furthermore, comparative molecular dynamics simulation (MDS), principal component (PC)-based free energy landscape (FEL) analysis, and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) were employed to show enhanced structural stability, increased H-bond potential, and high binding affinity toward the target InhA. Moreover, the hot spot residues that contributed to the high binding energy profile and anchored the stability of the complexes were revealed with their individual interaction energy. The computational insights from this study provide potential avenues to combat TB through the multifaceted mode of action of these marine lead molecules, which can be further explored in future experimental investigations.

Second-site suppressor mutations reveal connection between the drug-binding pocket and nucleotide-binding domain 1 of human P-glycoprotein (ABCB1)

Human P-glycoprotein (P-gp) or ABCB1 is overexpressed in many cancers and has been implicated in altering the bioavailability of chemotherapeutic drugs due to their efflux, resulting in the development of chemoresistance. To elucidate the mechanistic aspects and structure-function relationships of P-gp, we previously utilized a tyrosine (Y)-enriched P-gp mutant (15Y) and demonstrated that at least 15 conserved residues in the drug-binding pocket of P-gp are responsible for optimal substrate interaction and transport. To further understand the role of these 15 residues, two new mutants were generated, namely 6Y with the substitution of six residues (F72, F303, I306, F314, F336 and L339) with Y in transmembrane domain (TMD) 1 and 9Y with nine substitutions (F732, F759, F770, F938, F942, M949, L975, F983 and F994) in TMD2. Although both the mutants were expressed at normal levels at the cell surface, the 6Y mutant failed to transport all the tested substrates except Bodipy-verapamil, whereas the 9Y mutant effluxed all tested substrates in a manner very similar to that of the wild-type protein. Further mutational analysis revealed that two second-site mutations, one in intracellular helix (ICH) 4 (F916Y) and one in the Q loop of nucleotide-binding domain (NBD) 1 (F480Y) restored the transport function of 6Y. Additional biochemical data and comparative molecular dynamics simulations of the 6Y and 6Y+F916Y mutant indicate that the Q-loop of NBD1 of P-gp communicates with the substrate-binding sites in the transmembrane region through ICH4.This is the first evidence for the existence of second-site suppressors in human P-gp that allow recovery of the loss of transport function caused by primary mutations. Further study of such mutations could facilitate mapping of the communication pathway between the substrate-binding pocket and the NBDs of P-gp and possibly other ABC drug transporters.

How ligands regulate the binding of PARP1 with DNA: Deciphering the mechanism at the molecular level.

The catalytic (CAT) domain is a key region of poly (ADP-ribose) polymerase 1 (PARP1), which has crucial interactions with inhibitors, DNA, and other domains of PARP1. To facilitate the development of potential inhibitors of PARP1, it is of great significance to clarify the differences in structural dynamics and key residues between CAT/inhibitors and DNA/PARP1/inhibitors through structure-based computational design. In this paper, conformational changes in PAPR1 and differences in key residue interactions induced by inhibitors were revealed at the molecular level by comparative molecular dynamics (MD) simulations and energy decomposition. On one hand, PARP1 inhibitors indirectly change some residues of the CAT domain which interact with DNA and other domains. Furthermore, the interaction between ligands and catalytic binding sites can be transferred to the DNA recognition domain of PARP1 by a strong negative correlation movement among multi-domains of PARP1. On the other hand, it is not reliable to use the binding energy of CAT/ligand as a measure of ligand activity, because it may in some cases differs greatly from the that of PARP1/DNA/ligand. For PARP1/DNA/ligand, the stronger the binding stability between the ligand and PARP1, the stronger the binding stability between PARP1 and DNA. The findings of this work can guide further novel inhibitor design and the structural modification of PARP1 through structure-based computational design.

Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations

The class Frizzled of G protein-coupled receptors (GPCRs), consisting of ten Frizzled (FZD1-10) paralogs and Smoothened, remains one of the most enigmatic GPCR families. This class mediates signaling predominantly through Disheveled (DVL) or heterotrimeric G proteins. However, the mechanisms underlying pathway selection are elusive. Here we employ a structure-driven mutagenesis approach in combination with an extensive panel of functional signaling readouts to investigate the importance of conserved state-stabilizing residues in FZD5 for signal specification. Similar data were obtained for FZD4 and FZD10 suggesting that our findings can be extrapolated to other members of the FZD family. Comparative molecular dynamics simulations of wild type and selected FZD5 mutants further support the concept that distinct conformational changes in FZDs specify the signal outcome. In conclusion, we find that FZD5 and FZDs in general prefer coupling to DVL rather than heterotrimeric G proteins and that distinct active state micro-switches in the receptor are essential for pathway selection arguing for conformational changes in the receptor protein defining transducer selectivity.

Mechanistic Elucidation of Activation/Deactivation Signal Transduction within Neurotensin Receptor 1 Triggered by 'Driver Chemical Groups' of Modulators: A Comparative Molecular Dynamics Simulation.

Small-molecule modulators of neurotensin receptor 1 (NTSR1), a class A G-protein-coupled receptor (GPCR), has emerged as promising therapeutic agent for psychiatric disorders and cancer. Interestingly, a chemical group substitution in NTSR1 modulators can launch different types of downstream regulation, highlighting the significance of deciphering the internal fine-tuning mechanism. Here, we conducted a synergistic application of a Gaussian accelerated molecular dynamics simulation, a conventional molecular dynamics simulation, and Markov state models (MSM) to investigate the underlying mechanism of 'driver chemical groups' of modulators triggering inverse signaling. The results indicated that the flexibility of the leucine moiety in NTSR1 agonists contributes to the inward displacement of TM7 through a loosely coupled allosteric pathway, while the rigidity of the adamantane moiety in NTSR1 antagonists leads to unfavorable downward transduction of agonistic signaling. Furthermore, we found that R3226.54, Y3196.51, F3537.42, R1483.32, S3567.45, and S3577.46 may play a key role in inducing the activation of NTSR1. Together, our findings not only highlight the ingenious signal transduction within class A GPCRs but also lay a foundation for the development of targeted drugs harboring different regulatory functions of NTSR1.

Development, validation and analysis of a human profurin 3D model using comparative modeling and molecular dynamics simulations

The emergence of new viruses can lead to the outbreak of pandemics as occurred at the end of 2019 with the coronavirus disease (or COVID-19). The fastest way to effectively control viral infections is to develop broad-spectrum antivirals that can fight at least an entire class of viruses. Profurin, the furin precursor propeptide, is responsible for the autoactivation step which is crucial for the maturation of several viral substrates. This role makes the study of furin and profurin interactions interesting for the development of new potential broad-spectrum antivirals for the treatment against several human viral diseases. Since there is no 3D model of profurin published in the literature or deposited in a database, this work reports the development, validation and analysis of a profurin 3D model using comparative modeling and molecular dynamics. The model is available in ModelArchive at https://www.modelarchive.org/doi/10.5452/ma-ct8l7. The usage of this model will make possible further studies of molecular docking and MD simulations of the profurin-furin system, in the design of new potential broad-spectrum antivirals for the treatment against several human viral diseases. Communicated by Ramaswamy H. Sarma

Investigation on liquid thermal conductivity of ethylene glycol (EG)/water mixtures: A comparative experimental and molecular dynamics simulation study

Ethylene glycol (EG) and water mixtures can be used as the antifreeze, refrigerant and coolant due to their good environmental, thermodynamic and transport performance. The mixture’s accurate thermal conductivity is indispensable for the optimal design of the relevant heat exchangers. However, thermal conductivity of EG/water mixtures is lacking and is seen to limit the further industrial application. In this paper, the transient hot wire method (THW) was used to measure the thermal conductivities of five EG/water mixtures (with ethylene glycol mass fraction wEG = 0, 0.25, 0.50, 0.75, 1.00) in the temperature range from 253.15 K to 353.15 K and pressures up to 8.0 MPa. A comparison was made between the present experimental data and literature values, yielding a good agreement. The AADs are within 2.65% for EG/water mixture systems. For convenience of engineering calculations, the present experimental data were correlated as a function of temperature and pressure. The average absolute deviations (AADs) between the experimental thermal conductivities and the calculations are 0.50%, 0.10%, 0.60%, 0.40% and 0.32% for mixture systems with ethylene glycol mass fraction wEG = 0.00, 0.25, 0.50, 0.75, 1.00, respectively. In addition, non-equilibrium molecular dynamics was applied to study the thermal conductivities of ethylene glycol/water binary mixtures based on PCFF (polymer consistent force field) and SPC/E (extended simple point charge) model, showing a good agreement with the experimental data. This study can provide fundamental thermal conductivity data for the heat transfer application of ethylene glycol aqueous solution in the industrial field.

Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers.

Polyglutamine expansion at the N-terminus of the huntingtin protein exon 1 (Htt-ex1) is closely associated with a number of neurodegenerative diseases, which result from the aggregation of the increased polyQ repeat. However, the underlying structures and aggregation mechanism are still poorly understood. We performed microsecond-long all-atom molecular dynamics simulations to study the folding and dimerization of Htt-ex1 (about 100 residues) with non-pathogenic and pathogenic polyQ lengths, and uncovered substantial differences. The non-pathogenic monomer adopts a long α-helix that includes most of the polyQ residues, which forms the interaction interface for dimerization, and a PPII-turn-PPII motif in the proline-rich region. In the pathogenic monomer, the polyQ region is disordered, leading to compact structures with many intra-protein interactions and the formation of short β-sheets. Dimerization can proceed via different modes, where those involving the N-terminal headpiece bury more hydrophobic residues and are thus more stable. Moreover, in the pathogenic Htt-ex1 dimers the proline-rich region interacts with the polyQ region, which slows the formation of β-sheets.

Molecular Dynamics Simulations Reveal the Conformational Transition of GH33 Sialidases.

Sialidases are increasingly used in the production of sialyloligosaccharides, a significant component of human milk oligosaccharides. Elucidating the catalytic mechanism of sialidases is critical for the rational design of better biocatalysts, thereby facilitating the industrial production of sialyloligosaccharides. Through comparative all-atom molecular dynamics simulations, we investigated the structural dynamics of sialidases in Glycoside Hydrolase family 33 (GH33). Interestingly, several sialidases displayed significant conformational transition and formed a new cleft in the simulations. The new cleft was adjacent to the innate active site of the enzyme, which serves to accommodate the glycosyl acceptor. Furthermore, the residues involved in the specific interactions with the substrate were evolutionarily conserved in the whole GH33 family, highlighting their key roles in the catalysis of GH33 sialidases. Our results enriched the catalytic mechanism of GH33 sialidases, with potential implications in the rational design of sialidases.