Umbrella Sampling Molecular Dynamics Simulations Research Articles

Interaction of Hoechst 33342 with POPC Membranes at Different pH Values.

Hoechst 33342 (H33342) is a fluorescent probe that is commonly used to stain the DNA of living cells. To do so, it needs to interact with and permeate through cell membranes, despite its high overall charge at physiological pH values. In this work, we address the effect of pH in the association of H33342 with lipid bilayers using a combined experimental and computational approach. The partition of H33342 to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid membranes was experimentally quantified using fluorescence spectroscopy and isothermal titration calorimetry (ITC) measurements. Quantum chemical calculations were performed to select the most stable isomer of H33342 for the overall charges 0, +1, and +2, expected to predominate across the 5 < pH < 10 range. The interaction of these isomers with POPC bilayers was then studied by both unrestrained and umbrella sampling molecular dynamics (MD) simulations. Both experimental results and computational free energy profiles indicate that the partition coefficient of H33342 displays a small variation over a wide pH range, not exceeding one order of magnitude. The enthalpy variation upon partition to the membrane suggests efficient hydrogen bonding between the probe and the lipid, namely, for the protonated +2 form, which was confirmed in the MD simulation studies. The relatively high lipophilicity obtained for the charged species contrasts with the decrease in their general hydrophobicity as estimated from octanol/water partition. This highlights the distinction between lipophilicity and hydrophobicity, as well as the importance of considering the association with lipid bilayers when predicting the affinity for biomembranes.

Origin of the kinetic HDAC2-selectivity of an HDAC inhibitor.

A newly synthesized small molecule, KTT-1, exhibits kinetically selective inhibition of histone deacetylase 2, HDAC2, over its homologous enzyme, HDAC1. KTT-1 is hard to be released from the HDAC2/KTT-1 complex, compared to the HDAC1/KTT-1 complex and the residence time of KTT-1 in HDAC2 is longer than that in HDAC1. To explore the physical origin of this kinetic selectivity, we performed replica-exchange umbrella sampling molecular dynamics simulations for formation of both complexes. The calculated potentials of mean force suggest that KTT-1 is stably bound to HDAC2 and that it is easily disassociated from HDAC1. In the direct vicinity of the KTT-1 binding site in both enzymes, there exists a conserved loop consisting of four consecutive glycine residues (Gly304-307 for HDAC2; Gly299-302 for HDA1). The difference between the two enzymes comes from a single un-conserved residue behind this loop, namely, Ala268 in HDAC2 and Ser263 in HDAC1. The Ala268 contributes to the tight binding of KTT-1 to HDAC2 by the linear orientation of Ala268, Gly306, and one carbon atom in KTT-1. On the other hand, Ser263 cannot stabilize the binding of KTT-1 to HDAC1, because it is relatively further away from the glycine loop and because the directions of the two forces are not in line.

Mechanism of Chiral-Selective Aminoacylation of an RNA Minihelix Explored by QM/MM Free-Energy Simulations.

Aminoacylation of a primordial RNA minihelix composed of D-ribose shows L-amino acid preference over D-amino acid without any ribozymes or enzymes. This preference in the amino acylation reaction likely plays an important role in the establishment of homochirality in L-amino acid in modern proteins. However, molecular mechanisms of the chiral selective reaction remain unsolved mainly because of difficulty in direct observation of the reaction at the molecular scale by experiments. For seeking a possible mechanism of the chiral selectivity, quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations of the aminoacylation reactions in a modeled RNA were performed to investigate differences in their free-energy profiles along the reactions for L- and D-alanine and its physicochemical origin. The reaction is initiated by approaching a 3'-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. The QM/MM umbrella sampling MD calculations showed that the height of the free-energy barrier for L-alanine aminoacylation reaction was 17 kcal/mol, which was 9 kcal/mol lower than that for the D-alanine system. At the transition state, the distance between the negatively charged 3'-oxygen and the positively charged amino group of L-alanine was shorter than that of D-alanine, which was caused by the chirality difference of the amino acid. These results indicate that the transition state for L-alanine is more electrostatically stabilized than that for D-alanine, which would be a plausible mechanism previously unexplained for chiral selectivity in the RNA minihelix aminoacylation.

A comparative study on inclusion complex formation between formononetin and β-cyclodextrin derivatives through multiscale classical and umbrella sampling simulations

Formononetin, a naturally occurring isoflavone exhibits a wide range of therapeutic applications including antioxidant, anti-tumor, antiviral, anti-diabetic and neuroprotective activities. However, the low hydro-solubility of formononetin has limited its prospective use in cosmetic, neutraceutical and pharmaceutical industries. Cyclodextrins (CDs), especially β-CD and its derivatives have emerged as promising agents to improve the water solubility of poorly hydrosoluble compounds by the formation of inclusion complexes. We employed multiscale (1000 ns) explicit solvent and umbrella sampling molecular dynamics (MD) simulations to study the interactions and thermodynamic parameters of inclusion complex formation between formononetin and five most commonly used β-CD derivatives. Classical MD simulations revealed two possible binding conformations of formononetin inside the central cavity of hydroxypropyl-β-CD (HP-β-CD), randomly methylated-β-CD (ME-β-CD), and sulfobutylether-β-CD (SBE-β-CD). The binding conformation with the benzopyrone ring of formononetin inside the central cavity of β-CD derivatives was more frequent than the phenyl group occupying the hydrophobic cavity. These interactions were supported by a variety of non-bonded contacts including hydrogen bonds, pi-lone pair, pi-sigma, and pi-alkyl interactions. Formononetin showed favorable end-state MD-driven thermodynamic binding free energies with all the selected β-CD derivatives, except succinyl-β-CD (S-β-CD). Furthermore, umbrella sampling simulations were used to investigate the interactions and thermodynamic parameters of the host-guest inclusion complexes. The SBE-β-CD/formononetin inclusion complex showed the lowest binding energy signifying the highest affinity among all the selected host-guest inclusion complexes. Our study could be used as a standard for analyzing and comparing the ability of different β-CD derivatives to enhance the hydro-solubility of poorly soluble molecules.

Complex role of chemical nature and tacticity in the adsorption free energy of carboxylic acid polymers at the oil-water interface: molecular dynamics simulations.

Scientific understanding of the molecular structure and adsorption of polymers at oil-water liquid interfaces is very limited. In this study the adsorption free energy at the oil (CCl4)-water interface was estimated using umbrella sampling molecular dynamics simulations for six carboxylate type vinyl polymers differing in hydrophobic nature and tacticity: isotactic and syndiotactic poly(acrylic acid) (i-PAA, s-PAA), isotactic and syndiotactic poly(methacrylic acid) (i-PMA, s-PMA), and atactic and syndiotactic poly(ethylacrylic acid) (a-PEA, s-PEA). ΔGads values are in the order i-PMA < a-PEA < s-PEA < s-PAA < i-PAA < s-PMA. The results show the significant and complex influence of the chemical nature as well as tacticity of the polymer on its adsorption free energy as related to hydrogen bonding and orientation of bonds with respect to oil and water phases. The influence of tacticity is found to be the highest for PMA, which is interpreted to occur due to the balance between interactions among side groups and those occurring between side groups and solvent. Interactions between side-groups are crucial for determining the conformation of PAA (most hydrophilic) and the solvation of the side-group in water is crucial for determining the conformation of PEA (most hydrophobic). The adsorption of PMA represents the transition between these two dominating effects. The molecular contributions to the enthalpy of adsorption indicate that adsorption is favored mainly through two interactions: polymer-CCl4 and water-water.

Computational Evaluation of Peptide-Protein Binding Affinities: Application of Potential of Mean Force Calculations to SH2 Domains.

Many biological functions are mediated by protein-protein interactions (PPIs), often involving specific structural modules, such as SH2 domains. Inhibition of PPIs is a pharmaceutical strategy of growing importance. However, a major challenge in the design of PPI inhibitors is the large interface involved in these interactions, which, in many cases, makes inhibition by small organic molecules ineffective. Peptides, which cover a wide range of dimensions and can be opportunely designed to mimic protein sequences at PPI interfaces, represent a valuable alternative to small molecules. Computational techniques able to predict the binding affinity of peptides for the target domain or protein represent a crucial stage in the workflow for the design of peptide-based drugs. This chapter describes a protocol to obtain the potential of mean force (PMF) for peptide-SH2 domain binding, starting from umbrella sampling (US) molecular dynamics (MD) simulations. The PMF profiles can be effectively used to predict the relative standard binding free energies of different peptide sequences.

Computational characterization of homologous ligands binding to a deep hydrophobic pocket in Shigella flexneri pilot protein MxiM.

The type III secretion system (T3SS) is an important molecular machinery in gram-negative bacteria Shigella flexneri as it provides ways for translocating virulence factors from the bacteria into host cells, eventually leading to severe disease symptoms such as bacillary dysentery. Due to the rising concerns of antibiotics resistance in bactericidal strategy, the anti-virulence strategy that primarily targets the T3SS components becomes an attractive alternative. MxiM, the secretin pilot protein of Shigella flexneri, binds the secretin MxiD and facilitates the formation of the secretin ring in outer membrane in T3SS assembly. MxiM harbors a large hydrophobic pocket that has been shown to be important in MxiM-MxiD interaction. In this work, I examined the ligand binding property of MxiM by performing molecular dynamics (MD) simulations of the association between MxiM and a series of hydrophobic ligands, with simulation time amounted to 30 μs. MD simulations successfully captured spontaneous ligand binding events in 153 of the 300 trajectories. The ligand binding can be categorized into two types: a fast type, in which the ligand binds quickly into the hydrophobic pocket and a slow type, in which the ligand forms an encounter complex with the protein before binding into the hydrophobic pocket. Using the MxiM-ligand binding poses captured in MD simulations, I additionally performed umbrella-sampling MD simulations with total simulation time amounted to 63 μs to obtain protein-ligand binding free energies. The relationship between the ligand binding free energy and ligand size appears to be nonlinear and exhibits an exponential decay pattern. In summary, I performed computational characterization of MxiM-hydrophobic ligand binding capabilities and properties, which may provide valuable insights into designing anti-bacterial medicine against antibiotics resistance in Shigella flexneri.

A lesson for the maestro of the replication fork: Targeting the protein‐binding interface of proliferating cell nuclear antigen for anticancer therapy

The proliferating cell nuclear antigen (PCNA) has emerged as a promising candidate for the development of novel cancer therapeutics. PCNA is a nononcogenic mediator of DNA replication that regulates a diverse range of cellular functions and pathways through a comprehensive list of protein-protein interactions. The hydrophobic binding pocket on PCNA offers an opportunity for the development of inhibitors to target various types of cancers and modulate protein-protein interactions. In the present study, we explored the binding modes and affinity of molecule I1 (standard molecule) with the previously suggested dimer interface pocket and the hydrophobic pocket present on the frontal side of the PCNA monomer. We also identified potential lead molecules from the library of in-house synthesized 3-methylenisoindolin-1-one based molecules to inhibit the protein-protein interactions of PCNA. Our results were based on robust computational methods, including molecular docking, conventional, steered, and umbrella sampling molecular dynamics simulations. Our results suggested that the standard inhibitor I1 interacts with the hydrophobic pocket of PCNA with a higher affinity than the previously suggested binding site. Also, the proposed molecules showed better or comparable binding free energies as calculated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach and further validated by enhanced umbrella sampling simulations. In vitro and in vivo methods could test the computationally suggested molecules for advancement in the drug discovery pipeline.

Molecular Context of Dopa Influences Adhesion of Mussel-Inspired Peptides.

Improving adhesives for wet surfaces is an ongoing challenge. While the adhesive proteins of marine mussels have inspired many synthetic wet adhesives, the mechanisms of mussel adhesion are still not fully understood. Using surface forces apparatus (SFA) measurements and replica-exchange and umbrella-sampling molecular dynamics simulations, we probed the relationships between the sequence, structure, and adhesion of mussel-inspired peptides. Experimental and computational results reveal that peptides derived from mussel foot protein 3 slow (mfp-3s) containing 3,4-dihydroxyphenylalanine (Dopa), a post-translationally modified variant of tyrosine commonly found in mussel foot proteins, form adhesive monolayers on mica. In contrast, peptides with tyrosine adsorb as weakly adhesive clusters. We further considered simulations of mfp-3s derivatives on a range of hydrophobic and hydrophilic organic and inorganic surfaces (including silica, self-assembled monolayers, and a lipid bilayer) and demonstrated that the chemical character of the target surface and proximity of cationic and hydrophobic residues to Dopa affect peptide adsorption and adhesion. Collectively, our results suggest that conversion of tyrosine to Dopa in hydrophobic, sparsely charged peptides influences peptide self-association and ultimately dictates their adhesive performance.

Reaction Mechanism of MHETase, a PET Degrading Enzyme

In 2016, one of the two enzymes involved in the polyethylene terephthalate (PET) degradation pathway of Ideonella sakaiensis 201-F6, MHETase, was found to exhibit a strong ability to degrade the PET monomer mono-(2-hydroxyethyl)terephthalate (MHET) at room temperature, converting it back into the precursors used in PET production. MHETase engineering to improve efficiency is an active field that suffers from an incomplete characterization of its reaction mechanism. In this paper, we analyze the reaction mechanism of MHETase using umbrella sampling molecular dynamics simulations at the B3LYP/MM level of theory. The combination of a high theoretical level and extensive sampling generated a very robust computational prediction. We found that MHETase catalyzed the conversion of MHET in two steps, with a rate-limiting step activation barrier of ΔG⧧ = 19.35 ± 0.15 kcal·mol–1 (from the weighted-histogram analysis). Our calculations are in line with the hypothesis that a transient tetrahedral intermediate mediates the reaction mechanism in each step, which is quite common in the serine hydrolase class. The energy of the first tetrahedral intermediate was similar to that of the reactant state, while the tetrahedral intermediate of the deacylation step was observed to lie closer to the rate-limiting transition state. Nevertheless, both determined tetrahedral states were found to be transient, with activation barriers close to ∼2.0 kcal·mol–1 relative to the product state of the acylation and deacylation steps, corresponding to a half-life of about 3 ps at 303.15 K.

Predicting the Membrane Permeability of Fentanyl and Its Analogues by Molecular Dynamics Simulations

The lipid membrane is considered a crucial component of opioid general anesthesia. The main drug used for the induction and maintenance of opioid anesthesia is fentanyl and its various analogues. However, these drugs have different clinical effects, and detailed atomic-level insight into the drug–membrane interactions could lead to a better understanding how these drugs exert their anesthetic properties. In this study, we have used extensive umbrella sampling molecular dynamics simulations to study the permeation process of fentanyl and three of its analogues into a variety of simple phospholipid membrane models. Our simulations show that we can accurately predict the permeability coefficients of these drug molecules, which is an important process in understanding how pharmaceuticals reach their molecular targets. We were also able to show that one phospholipid provides more accurate predictions than other lipids commonly used in these types of permeation studies, which will aid future studies of these types of processes.

Surfactant desorption and scission free energies for cylindrical and spherical micelles from umbrella-sampling molecular dynamics simulations

HypothesisThe free energies associated with adsorption/desorption of individual surfactants from micelles and the fusion/scission of long micelles can be used to estimate the rate constants for micellar kinetics as functions of surfactant and salt concentration. ExperimentsWe compute the escape free energies △Gesc of surfactant from micelles and the scission free energies △Gsciss of long micelles from coarse-grained molecular dynamics simulations coupled with umbrella sampling, for micelles of both sodium dodecylsulfate (SDS) in sodium chloride (NaCl) and cetyltrimethylammonium chloride (CTAC) in sodium salicylate (NaSal). FindingsFor spherical micelles, △Gesc values have maxima at certain aggregation numbers, and at salt-to-surfactant molar concentration ratios R near unity, consistent with experiments. For cylindrical micelles, SDS/NaCl shows a minimum, and CTAC/NaSal a maximum in △Gesc, both at R ~ 0.7, while △Gsciss of CTAC micelles also peaks at around R ~ 0.7 and that of SDS micelles increases monotonically with R. We explain the non-monotonic dependence of escape and scission free energies on R by a combination of electrostatic screening and the decrease of micelle radius with increasing R. Transitions from predominantly spherical to cylindrical micelles, and between adsorption/desorption and fusion/scission kinetics with changing salt concentration can be inferred from the free energies for CTAC/NaSal.

Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer.

We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aβ peptide fragments. Despite dissimilar sequences, their permeation shares significant common features. Computations of free energies and permeabilities show that partitioning of both peptides is highly unfavorable, ruling out passive transport. The peptides experience multiple rotational transitions within the bilayer and typically cause considerable lipid disorder and bilayer thinning. Near the bilayer midplane, they lose almost entirely their solvation shell and the interactions with the lipid headgroups. The peptides cause complex reorganization within the proximal bilayer region. Upon insertion, they induce striking cholesterol influx reversed by its depletion and the influx of DMPC when the peptides reach the midplane. The differences in partitioning mechanisms are due to the much higher polarity of KLVF peptide, the permeation of which is more unfavorable and which exclusively assumes vertical orientations within the bilayer. In contrast, VVIA positions itself flat between the leaflets, causing minor disorder and even thickening of the BBB-mimetic bilayer. Due to the high density of the cholesterol-rich BBB bilayer, the unfavorable work associated with the peptide insertion provides a significant, but not dominant, contribution to the partition free energy, which is still governed by dehydration and loss of peptide-headgroup interactions. Comparison with experiments indicates that KLVF and VVIA permeation is similar to that of proline tetrapeptide, mannitol, or cimetidine, all of which exhibit no passive transport.

Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics.

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.

Ionic Liquid for PEDOT:PSS Treatment. Ion Binding Free Energy in Water Revealing the Importance of Anion Hydrophobicity.

Water solubility of PEDOT:PSS conducting polymer is achieved by PSS at the expense of disturbing the crystallinity and electron mobility of PEDOT. Recently, PEDOT crystallinity and electron mobility have been improved by treating the PEDOT:PSS aqueous solution with 1-ethyl-3-methylimidazolium- (EMIM-) based ionic liquids (IL) EMIM:X. The amount of such improvement varies drastically with the anion X coupled to EMIM cation in the IL. Herein, using umbrella-sampling molecular dynamics simulations on the aqueous solutions of a minimal model of PEDOT:PSS mixed with various EMIM:X ILs, we show that the solvation of each ion in water plays a major role in the free energies of ion binding and exchange. Anions X efficient for the improvement are weakly stabilized by hydration (i.e., hydrophobic) and prefer binding to hydrophobic PEDOT than to hydrophilic EMIM, favoring the ion exchange. In order to fulfill our design principle, a quantitative criterion based on hydration free energy is proposed to select efficient hydrophobic anions X.

Collective Solvation and Transport at Tetrahydrofuran-Silica Interfaces for Separation of Aromatic Compounds: Insight from Molecular Dynamics Simulations.

We have performed umbrella sampling molecular dynamics simulations to study the separation mechanism of aromatic compounds at the tetrahydrofuran (THF)-methanol-silica interface by liquid chromatography. Solute molecules with different polarities (naphthol and naphthalene) are selected as representative aromatic compounds. For the polar solute (naphthol), the free energy profile shows a deep minimum near the THF-silica interface, suggesting strong interactions with the polar surface. When methanol is added to the interface, there is a sharp increase in naphthol's free energy minimum, and the corresponding diffusion dynamics also undergoes a dramatic change. These findings explain the fast separation mechanism in recent experiments of separating fused ring compounds in asphaltenes with liquid chromatography. Further solvation structure and orientation analysis suggest that apolar and polar solutes may find their own comfort zones several angstroms away from the interface, and their phenyl ring's orientations would undergo a parallel-to-perpendicular transition as the solute molecule moves away from the surface. Extending our simulation studies to systems with different solute concentrations reveals that there is a decrease in the adsorption free energy accompanied by enhanced surface diffusion as the solute concentration increases, which is related to the crowding in the interfacial layers. Our simulation analysis gives a detailed microscopic description of solute solvation and transport at the THF-silica chromatography interface and will be helpful for improving separation protocols in future applications.

In-silico drug repurposing study: Amprenavir, enalaprilat, and plerixafor, potential drugs for destabilizing the SARS-CoV-2 S-protein-angiotensin-converting enzyme 2 complex

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that leads to coronavirus disease (COVID-19) has put public health at risk in 2020. The spike protein (SP) in SARS-CoV-2 is primarily responsible for the attachment and entry of the virus into the cell, which binds to the angiotensin-converting enzyme 2 (ACE2). Owing to the lack of an effective therapy, drug repositioning is an opportunity to search for molecules with pharmacological potential for the treatment of COVID-19. In this study, three candidates with the potential to destabilize the SP-ACE2 complex are reported. Through molecular docking, 147 drugs were evaluated and their possible binding sites in the interface region of the SP-ACE2 complex and the SP of SARS-CoV-2 were identified. The five best candidate molecules were selected for molecular dynamics studies to observe changes in interactions between SP-ACE2 and ligands with the SP-ACE2 complex. Using umbrella sampling molecular dynamics simulations, the binding energy of SP with ACE2 (−29.58 kcal/mol) without ligands, and in complex with amprenavir (−20.13 kcal/mol), enalaprilat (–23.84 kcal/mol), and plerixafor (−19.72 kcal/mol) were calculated. These drugs are potential candidates for the treatment of COVID-19 as they destabilize the SP-ACE2 complex; the binding energy of SP is decreased in the presence of these drugs and may prevent the virus from entering the cell. Plerixafor is the drug with the greatest potential to destabilize the SP-ACE2 complex, followed by amprenavir and enalaprilat; thus, these three drugs are proposed for future in vitro and in vivo evaluations.

Dynamics and Barrier of Movements of Sodium and Potassium Ions Across the Oxytricha nova G-Quadruplex Core.

G-quadruplexes (GQs) are highly stable noncanonical forms of nucleic acids that are present in important genomic regions. The central core of the GQ is lined up by four closely spaced carbonyl groups from the G-quartets, and the resulting electrostatic repulsion is neutralized by the coordinating cations. In spite of several reports on GQ structure and cation-GQ interactions, the atomic- to molecular-level understanding of the ion dynamics and ion exchange in the GQ core is quite poor. Here, we attempt to elucidate the mechanism of Na+ and K+ binding to the GQ core and trace the exchange of these ions with the ions in bulk by means of all-atomic molecular dynamics (MD) simulations. One of the most studied GQs, Oxytricha nova telomeric G-quadruplex (OxyGQ), is taken as the representative GQ. Subsequently, umbrella sampling MD simulations were performed to elucidate the energetics of ion translocation from one end to the other end of the GQ central core. Our study highlights the importance of ion hydration for the uptake and correct positioning of the cations in the core. The free-energy landscape of ion transport has shown favorable in-plane binding of Na+ ions with GQ quartets, which matches very well with the crystal structure. The binding of K+ ions, on the other hand, was out-of-plane and its translocation required a larger barrier to cross.

Molecular Dynamics Simulations of Bimolecular Electron Transfer: Testing the Coulomb Term in the Weller Equation.

Reliable estimation of the driving force for photoinduced electron transfer between neutral reactants is of utmost importance for most practical applications of these reactions. The driving force is usually calculated from the Weller equation, which contains a Coulomb term, C, whose magnitude in polar solvents is debated. We have performed umbrella sampling molecular dynamics simulations to determine C from the potentials of mean force between neutral and ionic donor/acceptor pairs of different sizes in solvents of varying polarity. According to the simulations, C in polar solvents is a factor of 2 more negative than typically calculated according to the Weller equation. Use of the π-stack contact distance in the Weller equation instead of the van der Waals radius recovers the correct value of C, but this is mostly fortuitous due to the compensating effects of overestimating the dielectric screening at contact and neglecting both charge dilution and desolvation.

Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association

We report the free-energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here, we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free-energy profile also captured the crucial role of allosteric IN inhibitors in promoting multimerization and explained why several C-terminal domain mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation, the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, interprotein water molecules are expelled to the bulk, resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side-chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. Although the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.