Performed MD Simulations Research Articles

Simulations of Endplate AChRs: Agonist Site β-Sheet and M1 π-Helix

Fetal AChRs have agonist binding-sites at α-δ and α-γ subunit interfaces. Four residues in the complimentary (non-α) subunit were shown previously to determine α-δ (low affinity; LA) vs. α-γ (high-affinity; HA) ACh-binding properties, one in the β5- β5’ linker and 3 in loop E. We performed MD simulations of AChBP-based homology models of LA and HA binding sites to investigate structural differences that make these residues influence affinity. Orientation of the linker residue, hydrogen bond patterns and the dynamics of the complimentary subunit backbone were different in LA vs. HA structures. The RMSF of the β5’ linker and loop E were smaller in LA vs. HA, but those in the bottom half of the β hairpin, near the agonist, were larger (W55, a structural water and the agonist itself). LA was associated with a straighter hairpin, a less-dynamic β5’ linker, a shorter and less-dynamic loop E and a more-dynamic backbone near the core. We also used simulations to investigate a conserved proline kink in the M1 transmembrane helix that separates π- and α-helical segments (Purohit et al. 2015, J. Physiol. 593: 2851). A combination of all-atom and coarse-grained simulations were used to study C vs. O structures in related receptors (GluCl, GLIC and GlyR). In all three of these, the kink angle is shallower (∼7o in GLuCl) and the backbone energy more stable in O compared to C. Normal mode analyses suggest that straightening of the M1 kink is coupled with a bending motion in M2 that has been associated with channel-opening. The M1 π-helix appears to be an important, spring-loaded moving element in AChR gating.

The effect of imidazolium cations on the structure and activity of the Candida antarctica Lipase B enzyme in ionic liquids.

In order to understand how cations affect the structural changes and enzyme activity of Lipase B from Candida antarctica, we performed all-atom molecular dynamics simulations of CALB in four types of ionic liquids (ILs) with varying sizes of imidazolium cations and correlated these results with the experimentally determined CALB activity. The imidazolium cations under study differ in the alkyl tail length in the following order: [Emim](+) < [Bmim](+) < [Hmim](+) < [Omim](+). We observed that the best enzyme activity and structural stability of CALB are obtained in [Bmim][TfO] and [Hmim][TfO]. In contrast, in [Emim][TfO], bonding of [TfO](-) to LYS-290 disrupts the interactions between LYS-290 and ILE-285, which leads to a closed catalytic gate conformation with low accessibility of substrates to the catalytic triad. In [Omim][TfO], strong hydrophobic interactions between [Omim](+) and LEU-278 result in a significant loss of the secondary structure of the α-10 helix and cause the exposure of the catalytic triad to ILs, which affects the stability of the catalytic triad and consequently deteriorates the enzyme activity. Overall, our study indicates that a high ion coordination number ([Emim][TfO]) or the presence of a long hydrophobic tail ([Omim][TfO]) can facilitate ion-protein interactions that cause structural distortions and a decrease in CALB enzyme activity in ILs.

Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins.

Despite decades of investigations, the principal mechanisms responsible for the high affinity and specificity of proteins for key physiological cations K+, Na+, and Ca2+ remain a hotly debated topic. At the core of the debate is an apparent need (or lack thereof) for an accurate description of the electrostatic response of the charge distribution in a protein to the binding of an ion. These effects range from partial electronic polarization of the directly ligating atoms to long-range effects related to partial charge transfer and electronic delocalization effects. While accurate modeling of cation recognition by metalloproteins warrants the use of quantum-mechanics (QM) calculations, the most popular approximations used in major biomolecular simulation packages rely on the implicit modeling of electronic polarization effects. That is, high-level QM computations for ion binding to proteins are desirable, but they are often unfeasible, because of the large size of the reactive-site models and the need to sample conformational space exhaustively at finite temperature. Several solutions to this challenge have been proposed in the field, ranging from the recently developed Drude polarizable force-field for simulations of metalloproteins to approximate tight-binding density functional theory (DFTB). To delineate the usefulness of different approximations, we examined the accuracy of three recent and commonly used theoretical models and numerical algorithms, namely, CHARMM C36, the latest developed Drude polarizable force fields, and DFTB3 with the latest 3OB parameters. We performed MD simulations for 30 cation-selective proteins with high-resolution X-ray structures to create ensembles of structures for analysis with different levels of theory, e.g., additive and polarizable force fields, DFTB3, and DFT. The results from DFT computations were used to benchmark CHARMM C36, Drude, and DFTB3 performance. The explicit modeling of quantum effects unveils the key electrostatic properties of the protein sites and the importance of specific ion-protein interactions. One of the most interesting findings is that secondary coordination shells of proteins are noticeably perturbed in a cation-dependent manner, showing significant delocalization and long-range effects of charge transfer and polarization upon binding Ca2+.

Position-dependent mechanical responses of nanoindented graphene nanoribbons: Molecular dynamics study

We performed MD simulations of nanoindentation on a single layer graphene nanoribbon in order to obtain the tip-position-dependent mechanical properties of the graphene nanoribbon. A correlation between the load and the indentation depth was constructed. Also, the bending rigidity, the Young’s modulus and the strength of the graphene nanoribbon were obtained. Our results yielded the tip position dependence of the Young’s modulus for the graphene nanoribbon. The Young’s modulus of the graphene nanoribbon was calculated by using the lowest value when the tip’s position was in the center region of the graphene nanoribbon, and as the tip’s position moved away from the center, the Young’s modulus increased. These results gave interesting insight as to why the Young’s moduli obtained from experiments were different from one another. The change in the mechanical properties of the graphene nanoribbon due to the change in the tip’s position can also lead to a novel graphene-based nanoelectromechanical device.

Investigation of thermodynamic, dynamic, and structural properties of H2 adsorption on a Ag-Au nanoalloy with a carbon nanotube support.

We have performed MD simulations to investigate H(2) adsorption on Ag-Au nanoclusters with the different Au mole fractions supported on the carbon nanotubes with the different diameters. Our thermodynamic results shown that the saturation value of coverage and the enthalpy of adsorption increases as the mole fraction of Au is increased. Our structural results showed that the presence of the H(2) gas exerts a significant effect on the nanocluster surface atoms and tends to stabilize the surface atoms on the nanocluster. Also, the structural changes are irreversible in such a way that by gradually decreasing the pressure to zero, the nanocluster geometry is not reversed to its initial structure in vacuum conditions. We have also shown that the nanoclusters have smaller values of the self-diffusion coefficients in presence of H(2) molecules than those values in the initial state (vacuum), which is due to the increasing of the interface structure between the nanocluster and the nanotube.

Viral mechanisms: Tat modulates DAT.

HIV-associated neurocognitive disorders (HANDs) are a set of neurological disorders including HIV encephalopathy and HIV dementia, which are associated with HIV-1 infection, and specifically with the HIV Tat protein, which is present in the brain of HIV-1–infected patients. Tat is thought to inhibit neuronal communication by acting directly on neurotransmitter transporters such as the human dopamine transporter, hDAT. hDAT transports dopamine from the presynaptic cleft into presynaptic neurons during neurotransmission. Curiously, cocaine blocks this clearance of dopamine by acting directly on hDAT, so HANDs are further exacerbated in HIV-1–positive patients who abuse cocaine. To probe the mechanism of Tat action on hDAT, Yuan et al. used a hDAT homology model to dock Tat onto the transporter and performed MD simulations to probe the conformational state of hDAT bound to Tat. They found that of the three known conformational states of hDAT, Tat binds only the outward-open structure with favorable binding energies. The authors predicted that Tat binding would block the entry pathway of the dopamine substrate, thereby inhibiting dopamine clearance from the presynaptic cleft. As well, the authors were able to identify key intramolecular interactions between Tat and key hDAT residues, including a cation-π interaction involving Y470 of hDAT and two hydrogen-bonding interactions involving hDAT residues Y88 and K92. These interactions persisted throughout the MD simulations. To obtain experimental evidence for the mode of binding predicted by the computational experiments, the authors monitored the effect of Tat on dopamine uptake by hDAT bearing mutations of the key residues they defined. This mutational analysis verified the role of the aromatic ring of hDAT Y470 and therefore the existence of a cation-π interaction with Tat and the role of hydrogen bonding at Y88 and K92. These results suggest a mechanism for how infection by HIV-1 leads to HANDs.

Molecular dynamics of the asymmetric dimers of EGFR: Simulations on the active and inactive conformations of the kinase domain

Abnormal activation of EGFR is associated with human cancer, and thus it is a key target for inhibition in cancer therapy. There is evidence suggesting that the activation mechanism of EGFR is based upon the formation of the asymmetric dimer of the kinase domains. Here, we performed MD simulations on the asymmetric dimer for both active and inactive conformations of EGFR kinase domain to investigate flexibility and intrinsic motions of the proteins. Simulations of the active conformation showed that the formation of the asymmetric dimer changes the dynamics of EGFR kinase domain by suppressing fluctuation of the protein and altering the direction of motion of the protein. In contrast, the asymmetric dimerization of the inactive conformation does not alter the overall fluctuation of the kinase domain and does not initiate destabilizing of the inactive structure. We also investigated the intermolecular interactions in the EGFR asymmetric dimers and found that in the active conformation the interactions are dominated by loop–loop contacts rather than those from the helix–helix interactions. In contrast, helix–helix interaction seemed to be more significant for the inactive kinase structure. This work helps us to better understand the conformational flexibility and dynamics of the EGFR kinase domain, as well as provides information that may be useful to develop newer classes of inhibitors that can block allosteric sites rather than the more traditional catalytic site.

N-3 PUFA-Containing Phospholipids Studied by MD Simulations: A Comparison of EPA, DPA and DHA

A wide range of health benefits is associated with consuming omega-3 polyunsaturated fatty acids (n-3 PUFA) from marine oils. Eicosapentaenoic acid (EPA, 20:5), its metabolite docosapentaenoic acid (DPA, 22:5) and docosahexaenoic acid (DHA, 22:6) are the major n-3 PUFAs derived primarily from dietary consumption. Whether their effects on health are shared or complementary is a matter of current debate. To understand how molecular organization within cell membranes responds to the incorporation of each n-3 PUFA into phospholipids, we are performing MD simulations on model membrane systems composed of 1-stearoyl-2-eicosapentaenoylphosphatidylcholine (18:0-20:5PC), 1-stearoyl-2-docosapentaenoylphosphatidylcholine (18:0-22:5PC), 1-stearoyl-2-docoshexaenoylphosphatidylcholine (18:0-22:6PC) and, as a monounsaturated comparison, 1-stearoyl-2-oleoylphosphatidylcholine (SOPC, 18:0-18:1PC) in the absence and presence of cholesterol.

Quantifying the Stability of Acridines to Ribosomal G-Quadruplexes

G-quadruplexes are involved in fundamental regulatory processes, including those associated with cancer. Previous studies primarily focused on telomeric and oncogenic DNA G-quadruplexes, but recent studies have demonstrated that G-quadruplexes in ribosomal DNA or ribosomal RNA (rDNA or rRNA), may be an alternative target with a significant clinical potential through the inhibition of RNA polymerase I (Pol I) in ribosome biogenesis. The structures of ribosomal G-quadruplexes at atomic resolution are unknown and very little biophysical characterization has been performed on them. In our present study, we modeled putative ribosomal G-quadruplexes that were previously predicted using a bioinformatics algorithm and verified using CD spectroscopy to exist in a predominantly parallel topology. To quantify the relative stabilities of the acridine:G-quadruplex structures, we introduce two novel metrics for quantifying the relative stability of the G-quadruplex tetrads: 1) the center of mass base-to-base distance between diagonal guanines, and 2) the torsional angle between four guanines. Our relative free energy profiles show that the rDNA G-quadruplex structures with shorter loops are more stable for parallel topologies. The antiparallel topology was determined adopt a disordered configuration due to the lack of planarity after the simulation. To evaluate acridine molecules as a viable small molecule chemotherapeutic agent, we then rationally designed several acridine molecules. Each has a polyaromatic face that binds to the top-most G-tetrad and has amino or carboxyl side-chains to selectively optimize the shape and electrostatic complementarity. We then docked acridines to the rDNA G-quadruplexes and performed MD simulations. We identified several acridines with amino groups, and the nature of their specificity and relative stabilities depend on the rDNA G-quadruplex loop structures.

Molecular Dynamics Simulations on the Periplasmic-Open State Lactose Permease

Lactose Permease (LacY) is a secondary active transporter (SAT) that belongs to major facilitator superfamily (MFS). LacY structures of the cytoplasmic-open and more recently occluded-like structure have been determined. The structure of periplasmic-open LacY is important for understanding complete proton/sugar transport of LacY as well as other similar transporters. Though the exact structure of periplasmic-open LacY has not been obtained experimentally, a few molecular models have been determined. Previously, Pendse et al. (JMB, 404: 506-521) obtained a periplasmic-open LacY model through a two-step hybrid implicit-explicit (IM-EX) simulation method. Radestock et al. (JMB, 407: 698-715) proposed two new periplasmic-open LacY models by swapping inverted-topology repeats and adopting the outward L-fucose-proton symporter (fucP) crystal structure. The accuracy of these three periplasmic-open state models are tested by performing MD simulations on LacY-apo and LacY-ββ-(Galp)2. The comparison of the calculated pore radii to the data of the crystal structure indicates that the IM-EX model of LacY remains in periplasmic-open state. However, Radestock et al.'s models close on the periplasmic side and partially close on the cytoplasmic side, which indicates these two outward LacY models are unstable. Compared to the DEER experimental data, the selected residue pair distance changes demonstrates that the repeat-swapped LacY seems to be in the occluded state by 100ns. We will run MD simulations with labeled residues to directly compare with DEER for the IM-EX model to verify the effects of the spin label size and orientation on the accuracy of the distance measurement.

Molecular Details of the Mechanism of PS Recognition by TIM Proteins

Accumulating evidence suggests that an immune response can be triggered by the presence of abnormal lipid components, such as phosphatidylserine (PS), in the outer leaflet of the cellular membrane. The T-cell immunoglobulin and mucin domain (TIM) family of proteins recognize PS exposed on the surface of the membrane. TIM proteins are expressed by numerous cell types, and despite their close structural similarity, they are involved in triggering different immune responses. These specific roles have been attributed to different factors, including differential binding modes of TIM proteins to anionic membranes and their variable sensitivity to lipid composition of the membrane.In order to study the mechanism of membrane binding by TIM proteins, we have performed MD simulations of TIM1 and TIM3 employing our enhanced-dynamics HMMM membrane model. For each protein, we have performed a total of 30 independent simulations with different lipid compositions (1:1 PC:PS and 7:3 PC:PS), providing robust statistics to characterize the membrane-bound form of these proteins. The results suggest that, despite the overall structural similarity, TIM1 and TIM3 establish different interactions with the membrane upon binding. Moreover, simulations show that in addition to the PS-binding pocket found in TIM proteins, other specific protein-membrane ionic interactions can be formed in each case, suggesting a molecular basis for their different biological roles.In addition to MD simulations, the orientation of TIM1 and TIM3 in model PS-containing membranes has been characterized using X-ray scattering. The agreement between the X-ray experiments and the MD simulations provide a detailed description of the membrane-binding mechanism of TIM proteins.

Research/review: Structure and linkage disequilibrium analysis of adamantane resistant mutations in influenza virus m2 proton channel.

The M2 proton channel is translated by the M gene segment of influenza viruses, and has been adopted as an attractive target for influenza A viruses, on which a series of adamantane-based drugs act. However, recently epidemic influenza viruses have had strong resistant effects against the adamantane-based drugs. In this paper, we combined evolutionary analyses, linkage disequilibrium as well as molecular dynamics simulations to explore the drug resistance of the M2 proton channel, with an aim of providing an in-depth understanding of the resistant mechanism for adamantane-based drugs. We collected 2746 coding sequences for swine, avian, and human M2 proteins. After evolutionary and linkage disequilibrium analyses, we found that the some residues in the C-terminal were associated with the famed resistant mutation S31N. Subsequently, we constructed the 3D structures of the swine, avian as well as human M2 channel, and performed MD simulations on these channels with a typical adamantane-based drug rimantadine. From the simulation trajectories, we found that the resistance against the adamantane-based drugs for the M2 channel from 2009 A(H1N1) viruses was derived from the structural allostery in the transmembrane and C-terminal regions. The helices in the transmembrane region were irregular in formation and employed larger distances between the adjacent 2 helices, which can weaken the interactions between the adjacent 2 helices and destabilize the helix-helix assembly, resulting in a comparatively loosely structure. The helices in the C-terminal region show a disordered configuration, giving chances for solvent molecules to enter into the channel pore.

Property Evolution of ALD-Al2O3 Coated and Uncoated Si Electrodes

Introduction Rechargeable energy storage device are evolving as a major technological challenge when people are aiming its applications on a large scale, such as environmentally friendly electric vehicles or renewable energy storages. In spite of great deal of research, at present, reported energy density of lithium-ion batteries are significantly insufficient for the electric vehicle applications. Therefore, to meet the demand for the large scale applications, Silicon (Si) has long been considered a promising high capacity negative electrode in lithium ion batteries. However, the volume change up to ~300% for Si during lithiation and dilithiation leads to fracture of Si and/or loss of electrical contact with the conductive phase or the current collectors.The native SEI layer formed due to electrolyte decomposition can effectively passivate the graphite electrode (currently used in all Li-ion batteries) surface to prevent further side reactions with electrolyte, providing high coulombic efficiency.1,2 However, stabilizing SEI is much more difficult on Si than graphite due to the large volume change. A stable SEI should be able to mechanically accommodate the large volume in the underlying Si, while maintaining the passivation of the Si surfaces. Because the naturally formed native SEI cannot meet both criteria above, various artificial SEI layer have been designed to improve the performance and life of Li-ion batteries. Especially, atomic layer deposition (ALD) coatings have shown promising results to slow down or change the reduction process of EC electrolyte solvent and can also prevent mechanical failure of Si electrode.3 In order to develop a validated model to design coated Si electrode, it is critical to understand the mechanical and chemical stability of SEI in electrochemical environment, the correlation between coulombic efficiency and the dynamic process of SEI evolution and the structural optimization of both the SEI and the Si electrode. Therefore, to elucidate the underlying intricate chemistry, rigorous analysis at atomic level becomes necessary. This study will focus on comparing the ALD-Al2O3 coated Si surface with non-coated surface, which is typically terminated by native SiO2layer. Calculations and Results First, the composition evolution of Al2O3 and SiO2 layer within the voltage of 1~0.1V in a Li ion battery half-cell was computed from density functional theory (DFT). As shown in Table I, both SiO2 and Al2O3will be lithiated at the voltage above EC decomposition (~0.8V), contributing to the initial irreversible capacity loss.Thus, the mechanical property and Li diffusion were investigated for the lithiated aluminum oxide and lithiated Si oxide phases. The DFT predicted Youngs’ Modulus for crystalline Al2O3 coating is softened due to lithiation, while the change in SiO2layer is minimal. Both Li interstitial and Li vacancy can diffuse easily in Lithaited aluminum oxide and Si oxide phases.These DFT results were then used to guide the development of the reactive force field (ReaxFF) of Li-Si-O and Li-Al-O systems. More specifically, the ReaxFF was developed against to the open circuit voltage curve, vacancy formation energy, Li interstitial formation energy and their diffusion barriers in crystalline SiO2 and Al2O3structures. In order to understand the mechanical response and the diffusion properties of the coating layer on Si electrode upon litigation and delithiation, we further performed MD simulations with the ReaxFF.Table 1: Illustration of Al2O3 and SiO2covered Si electrode surface. (The data was based on crystalline form via DFT calculations).ObservationsBare Si electrodeALD coated electrodeLithiation Reaction2Li + SiO2 --> 0.5Li4SiO4 + 0.5Si <V> = 1.2V1.5Li+Al2O3 --> 1.5LiAlO2+0.5Al <V>=0.93VYoung’s Modules (GPa)*E(SiO2) = 140E(Li4SiO4 ) = 143E(Al2O3) =360E(LiAlO2)=150 Discussion The simulations results are compared with experimental modulus and kinetics measurements on ALD-Al2O3coated and uncoated Si thin film electrodes. Further exploration of the failure mechanism of the ALD coating on Si electrode will be discussed. References Y.S. Jung, A.S.Cavanagh, R.A. Leah, S.H.Kang, A.C.Dillon, M.D. Groner, S.M. George, and Y.H.Lee, Adv. Mater. 22, 2172 (2010)X. Xiao, P. Lu, D. Ahn, Adv. Mater. 23, 3911 (2011).K. Leung, Y. Qi, K. R. Zavadil, Y. S. Jung, A. C. Dillon, A. S. Cavanagh, S. Lee, and S. M. George, J. Am. Chem. Soc., 133, 14741 (2011)

The Coupling of Tension and Crowding Sensing in the Bacterial Channel MscS

Macromolecular excluded volume (crowding) is a critical parameter regulated by all cells, but how it is sensed remains unclear. Bacteria avoid dehydration in hypertonic media by accumulating ions and compatible osmolytes, which retain the necessary fraction of free water. Upon dilution of the medium, excess osmolytes are released through tension-activated channels acting as valves. We found that the mechanosensitive channel MscS, which exhibits slow inactivation under moderate tension, inactivates abruptly under the same tension in the presence of cytoplasmic crowders. To study the synergism between tension and crowding, we analyze the features that differentiate the inactivated (crystal-like) conformation from the modeled compact resting state, which include the splayed lipid-facing TM1-TM2 helices uncoupled from the gate and sharp kinks of the pore-lining TM3s at G113 stabilized by association of TM3b segments with the cytoplasmic beta domains. To mimic the effect of crowding, we performed MD simulations in which axial pressure is applied to the bottom of the cytoplasmic (cage) domain toward the membrane. We found that both models exhibit similar axial compliance and the cage reduces its volume in the cytoplasm, however in the inactivated state axial compaction produces a stronger expansion of the TM domain in the plane of the membrane. This concerted shape change appears to be the reason for the thermodynamic coupling of the bulk crowding effect with the energetic input from membrane tension, which both drive channel inactivation. We conclude that cage of MscS is the sensor which provides the feedback on increased crowding and disengages the gate to prevent c ‘over-draining’ of the cytoplasm. We discuss the mechanics of a bacterial cell surrounded by an elastic cell wall where this inhibitory feedback on osmolytes release might be necessary.

MD Simulations on Alpha-Tocopherol in PUFA Containing Lipid

Polyunsaturated fatty acids (PUFA) are an influential constituent in cell membranes, but are extremely vulnerable to oxidation. The presumptive role for α-tocopherol (α-toc), the molecular form of vitamin E retained by the human body, is to protect PUFA-containing lipids from oxidation. To investigate whether α-toc preferentially interacts with PUFA in support of this function, we performed MD simulations on lipid bilayers composed of 1-stearoyl-2-docosahexaenoylphosphatidylcholine (SDPC, 18:0-22-6PC) and 1-stearoyl-2-oleoylphosphatidylcholine (SOPC, 18:0-18:1PC) in the presence of α-toc. SDPC with docosahexaenoic acid (DHA) for the sn-2 chain is polyunsaturated, while SOPC with oleic acid (OA) for the sn-2 chain serves as a monounsaturated control. The simulations were run at 310 K under constant pressure for 200 ns on a system comprised of 80 phospholipid molecules, 20 α-toc molecules and 2165 water molecules. In qualitative agreement with our results from solid state 2H NMR and neutron scattering experiments, the simulations show that α-toc increases order inside the bilayer and that the chromanol headgroup sits near the surface in both SDPC and SOPC. Analyses of the density distribution of the lipid chains relative to α-toc are underway to determine differences in how α-toc associates with each chain. A major prediction from our simulations is that α-toc undergoes flip-flop across the bilayer, and that the rate is an order of magnitude greater in SDPC than SOPC. This is a remarkable finding that reveals a possible mechanism by which the chromanol group would not only wait at the membrane surface but would also patrol the membrane interior to meet lipid radicals and terminate the chain reaction by which lipid peroxidation proceeds.

A Single Inter-Domain Salt Bridge within the Human Argonaute 2 Protein Crucially Affects Protein Folding and Consequently Enzymatic Activity

RNA interference is a highly complex process involved in posttranscriptional gene regulation. Argonaute (Ago) proteins are the key component of the RNA-induced silencing complex (RISC) and mediate RNA interference (RNAi) in association with small RNAs. Ago2 proteins are composed of four domains: N, PAZ, Mid and PIWI, tethered by L1 and L2 linker regions [1, 2].In the binary complex of Ago2 and single stranded RNA, the 3'-end of the RNA is bound to the PAZ domain and the 5'-phosphate is anchored within a binding pocket in the Mid domain. The PIWI domain harbors the active site, which is composed of a catalytic tetrad as observed in RNase H.In the present study, we performed MD simulations on the hAgo2 protein in complex with a bound miRNA (pdb 4F3T). The protein undergoes prominent breathing motions dominated largely by movements of the PAZ and N domains. Most interestingly, we observed the transient formation a thitherto-undescribed inter-domain salt bridge. The introduction of a mutation preventing formation of this salt bridge drastically affected nucleic acid binding properties of recombinant hAgo2 [3] and abolished the enzymatic activity. In summary, the missing salt bridge not only affects overall protein conformation and stability but also seems to be crucial for proper positioning of the small RNA.1. Elkayam, E., et al., (2012) The structure of human Argonaute-2 in complex with miR-20a. Cell 150(1), 100-110.2. Schirle, N.T. and MacRae, I.J., (2012) The crystal structure of human Argonaute2. Science 336(6084), 1037-1040.3. Deerberg, A., et al., (2013) Minimal mechanistic model of siRNA-dependent target RNA slicing by recombinant human Argonaute 2 protein. PNAS in press.

Hydrodynamic interactions slow down crystallization of soft colloids.

Colloidal suspensions are often argued to be an ideal model for studying phase transitions such as crystallization, as they have the advantage of tunable interactions and experimentally tractable time and length scales. Because crystallization is assumed to be unaffected by details of particle transport other than the bulk diffusion coefficient, findings are frequently argued to be transferable to pure melts without solvent. In this article, we present molecular dynamics simulations of crystallization in a suspension of colloids with Yukawa interactions which challenge this assumption. In order to investigate the role of hydrodynamic interactions mediated by the solvent, we model the solvent both implicitly and explicitly, using Langevin dynamics and the fluctuating lattice Boltzmann method, respectively. Our simulations show a significant reduction of the crystal growth velocity due to hydrodynamic interactions even at moderate hydrodynamic coupling. This slowdown is accompanied by a reduction of the width of the layering region in front of the growing crystal. Thus the dynamics of a colloidal suspension differ strongly from that of a melt, making it less useful as a model for solvent-free melts than previously thought.

Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations

We investigate the structures of the Hras-GTP and the Hras-GDP complexes in water solvents in order to understand the mechanism of GTP hydrolysis in the Hras-GTP complex. We performed MD simulations of these complexes in order to study the positions and the orientations of water molecules around the guanosine nucleotides. Using trajectories we calculated the angular distribution of water molecules around the most distant phosphorus from guanosine in our previous work. It was shown that water molecules are distributed evenly in GTP, although unevenly in GDP. This suggests that the trigger of GTP hydrolysis is possibly the attack of water molecule to γ−phosphate from the appropriate direction. In this paper, in order to investigate the role of water molecules in GTP hydrolysis in detail, we calculate the orientation of water molecules. The distribution of the orientation is different between GTP and GDP. In order to investigate the cause of this difference, we examine the hydrogen bonds between water molecules and oxygen atom of the most distant phosphate from guanosine. We find that these hydrogen bonds are formed. We also find that the oxygen atom of hydrogen bond is determined by the position of the water molecule of hydrogen bond.

Stabilities and structures of islet amyloid polypeptide (IAPP22–28) oligomers: From dimer to 16-mer

BackgroundThe formation of amyloid fibrils is associated with many age-related degenerative diseases. Nevertheless, the molecular mechanism that directs the nucleation of these fibrils is not fully understood. MethodsHere, we performed MD simulations for the NFGAILS motif of hIAPP associated with the type II diabetes to estimate the stabilities of hIAPP22–28 protofibrils with different sizes: from 2 to 16 chains. In addition, to study the initial self-assembly stage, 4 and 8 IAPP22–28 chains in explicit solvent were also simulated. ResultsOur results indicate that the ordered protofibrils with no more than 16 hIAPP22–28 chains will be structurally stable in two layers, while one-layer or three-layer models are not stable as expected. Furthermore, the oligomerization simulations show that the initial coil structures of peptides can quickly aggregate and convert to partially ordered β-sheet-rich oligomers. ConclusionsBased on the obtained results, we found that the stability of an IAPP22–28 oligomer was not only related with its size but also with its morphology. The driving forces to form and stabilize an oligomer are the hydrophobic effects and backbone H-bond interaction. Our simulations also indicate that IAPP22–28 peptides tend to form an antiparallel strand orientation within the sheet. General significanceOur finding can not only enhance the understanding about potential mechanisms of hIAPP nuclei formation and the extensive structural polymorphisms of oligomers, but also provide valuable information to develop potential β-sheet formation inhibitors against type II diabetes.

Multiscale modeling and simulation of deformation in nanoscale metallic multilayer systems

Nanoscale metallic multilayers (NMM) have very high strength approaching a fraction of the theoretical limit. Their increased strength is attributed to the high interface density and is limited by the interfacial strength. As the density of interfaces increases (due to smaller layer thicknesses) the strength of NMM structures becomes increasingly determined by the specific nature and properties of the interfaces and is most likely controlled by the nucleation of dislocations from the interfaces. With focus on material systems with incoherent interfaces, we performed MD simulations to determine the controlling deformation mechanisms at different length scales for Cu–Nb multilayers under biaxial tensile deformation conditions. The results of the simulations show that there is a transition in the operative deformation mechanism in NMMs from Hall–Petch strengthening for the length scales of sub microns to microns, to individual dislocations confined to glide in individual layers for few nm to few tens of nm, and dislocation-nucleation-controlled models for less than few nanometers. Based on these results, we develop a Molecular dynamics-based rate-sensitive model for viscoplastic flow which describes the anisotropic deformation behavior of NMMs at different length scales.