Min Sun Yeom

CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

Strengthening effect of single-atomic-layer graphene in metal–graphene nanolayered composites

Graphene is a single-atomic-layer material with excellent mechanical properties and has the potential to enhance the strength of composites. Its two-dimensional geometry, high intrinsic strength and modulus can effectively constrain dislocation motion, resulting in the significant strengthening of metals. Here we demonstrate a new material design in the form of a nanolayered composite consisting of alternating layers of metal (copper or nickel) and monolayer graphene that has ultra-high strengths of 1.5 and 4.0 GPa for copper-graphene with 70-nm repeat layer spacing and nickel-graphene with 100-nm repeat layer spacing, respectively. The ultra-high strengths of these metal-graphene nanolayered structures indicate the effectiveness of graphene in blocking dislocation propagation across the metal-graphene interface. Ex situ and in situ transmission electron microscopy compression tests and molecular dynamics simulations confirm a build-up of dislocations at the graphene interface.

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics

Lipopolysaccharide (LPS), a component of Gram-negative bacterial outer membranes, comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. Using the CHARMM36 lipid and carbohydrate force fields, we have constructed a model of an Escherichia coli R1 (core) O6 (antigen) LPS molecule. Several all-atom bilayers are built and simulated with lipid A only (LIPA) and varying lengths of 0 (LPS0), 5 (LPS5), and 10 (LPS10) O6 antigen repeating units; a single unit of O6 antigen contains five sugar residues. From (1)H,(1)H-NOESY experiments, cross-relaxation rates are obtained from an O-antigen polysaccharide sample. Although some experimental deviations are due to spin-diffusion, the remaining effective proton-proton distances show generally very good agreement between NMR experiments and molecular dynamics simulations. The simulation results show that increasing the LPS molecular length has an impact on LPS structure and dynamics and also on LPS bilayer properties. Terminal residues in a LPS bilayer are more flexible and extended along the membrane normal. As the core and O-antigen are added, per-lipid area increases and lipid bilayer order decreases. In addition, results from mixed LPS0/5 and LPS0/10 bilayer simulations show that the LPS O-antigen conformations at a higher concentration of LPS5 and LPS10 are more orthogonal to the membrane and less flexible. The O-antigen concentration of mixed LPS bilayers does not have a significant effect on per-lipid area and hydrophobic thickness. Analysis of ion and water penetration shows that water molecules can penetrate inside the inner core region, and hydration is critical to maintain the integrity of the bilayer structure.

Loop Flexibility and Solvent Dynamics as Determinants for the Selective Inhibition of Cyclin-Dependent Kinase 4: Comparative Molecular Dynamics Simulation Studies of CDK2 and CDK4

The design and discovery of selective cyclin‐dependent kinase 4 (CDK4) inhibitors have been actively pursued in order to develop therapeutic cancer treatments. By means of a consecutive computational protocol involving homology modeling, docking experiments, and molecular dynamics simulations, we examine the characteristic structural and dynamic properties that distinguish CDK4 from CDK2 in its complexation with selective inhibitors. The results for all three CDK4‐selective inhibitors under investigation show that the large‐amplitude motion of a disordered loop of CDK4 is damped out in the presence of the inhibitors whereas their binding in the CDK2 active site has little effect on the loop flexibility. It is also found that the binding preference of CDK4‐ selective inhibitors for CDK4 over CDK2 stems from the reduced solvent accessibility in the active site of the former due to the formation of a stable hydrogen‐bond triad by the Asp99, Arg101, and Thr102 side chains at the top of the active‐site gorge. Besides the differences in loop flexibility and solvent accessibility, the dynamic stabilities of the hydrogen bonds between the inhibitors and the side chain of the lysine residue at the bottom of the active site also correlate well with the relative binding affinities of the inhibitors for the two CDKs. These results highlight the usefulness of this computational approach in evaluating the selectivity of a CDK inhibitor, and demonstrate the necessity of considering protein flexibility and solvent effects in designing new selective CDK4‐selective inhibitors.

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface

The outer membrane of Gram-negative bacteria is an asymmetric membrane with lipopolysaccharides on the external leaflet and phospholipids on the periplasmic leaflet. This outer membrane contains mainly β-barrel transmembrane proteins and lipidated periplasmic proteins (lipoproteins). The multisubunit protein β-barrel assembly machine (BAM) catalyzes the insertion and folding of the β-barrel proteins into this membrane. In Escherichia coli, the BAM complex consists of five subunits, a core transmembrane β-barrel with a long periplasmic domain (BamA) and four lipoproteins (BamB/C/D/E). The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs that are key to BAM complex formation and interaction with the substrate β-barrel proteins. The BAM complex is believed to undergo conformational cycling while facilitating insertion of client proteins into the outer membrane. Reports describing variable conformations and dynamics of the periplasmic POTRA domain have been published. Therefore, elucidation of the conformational dynamics of the POTRA domain in full-length BamA is important to understand the function of this molecular complex. Using molecular dynamics simulations, we present evidence that the conformational flexibility of the POTRA domain is modulated by binding to the periplasmic surface of a native lipid membrane. Furthermore, membrane binding of the POTRA domain is compatible with both BamB and BamD binding, suggesting that conformational selection of different POTRA domain conformations may be involved in the mechanism of BAM-facilitated insertion of outer membrane β-barrel proteins.

Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability

The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K(+) and Cl(-)), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.

Monte Carlo calculation of the ionization chamber response to 60Co beam using PENELOPE

The calculation of the ionization chamber response is one of key factors to develop a primary standard of air kerma. Using Monte Carlo code PENELOPE, we simulated the cavity response of the plane parallel ionization chamber to the monoenergetic 60Co beam incident normally on a flat surface of the chamber. Two simulation techniques, namely, the uniform interaction technique and the reentrance technique, were introduced. The effect of the input parameters such as C1 (average angular deflection in a single step between hard elastic events), C2 (maximum average fractional energy loss in a step), S(max) (maximum step length) and W(cc) (the lower energy of secondary electrons created as a result of a hard collision) on the simulated cavity dose was evaluated. We found that the simulated cavity response of the graphite and solid air chambers obtained by PENELOPE to the monoenergetic 60Co beam could be consistent with the value expected from the cross-sections of PENELOPE to within 0.2% (one standard deviation) when W(cc) and S(max) were selected carefully.

ST-analyzer: A web-based user interface for simulation trajectory analysis

Molecular dynamics (MD) simulation has become one of the key tools to obtain deeper insights into biological systems using various levels of descriptions such as all‐atom, united‐atom, and coarse‐grained models. Recent advances in computing resources and MD programs have significantly accelerated the simulation time and thus increased the amount of trajectory data. Although many laboratories routinely perform MD simulations, analyzing MD trajectories is still time consuming and often a difficult task. ST‐analyzer, http://im.bioinformatics.ku.edu/st‐analyzer, is a standalone graphical user interface (GUI) toolset to perform various trajectory analyses. ST‐analyzer has several outstanding features compared to other existing analysis tools: (i) handling various formats of trajectory files from MD programs, such as CHARMM, NAMD, GROMACS, and Amber, (ii) intuitive web‐based GUI environment—minimizing administrative load and reducing burdens on the user from adapting new software environments, (iii) platform independent design—working with any existing operating system, (iv) easy integration into job queuing systems—providing options of batch processing either on the cluster or in an interactive mode, and (v) providing independence between foreground GUI and background modules—making it easier to add personal modules or to recycle/integrate pre‐existing scripts utilizing other analysis tools. The current ST‐analyzer contains nine main analysis modules that together contain 18 options, including density profile, lipid deuterium order parameters, surface area per lipid, and membrane hydrophobic thickness. This article introduces ST‐analyzer with its design, implementation, and features, and also illustrates practical analysis of lipid bilayer simulations.

Polyselenide Anchoring Using Transition-Metal Disulfides for Enhanced Lithium–Selenium Batteries

While selenium has recently been proposed as a lithium battery cathode as a promising alternative to a lithium-sulfur battery, dissolution of intermediate species should be resolved to improve its cycle stability. Here, we report the promising results of transition-metal disulfides as an anchoring material and the underlying origin for preventing active material loss from the electrode using density functional theory calculations. Group 5 and 4 disulfides (VS2, NbS2, TaS2, TiS2, ZrS2, and HfS2) in particular show anchoring capabilities superior to those of group 6 disulfides (CrS2, MoS2, and WS2). The governing interaction controlling the latter relative anchoring strengths is shown to be charge transfer as understood by crystal-field theory. The current findings and methodologies provide novel chemical insight for the further design of inorganic anchoring materials for both lithium-selenium and lithium-sulfur batteries.

Analysis of shear-induced and extensional-induced associating polymer assemblies: Brownian dynamics simulation

In order to examine the difference between shear-induced and extensional-induced associating polymer assemblies at the molecular level, Brownian dynamics simulations with the bead-spring model were carried out for model DNA molecules with sticky spots. The radial distribution of molecules overestimates from that in the absence of flow and increases with increasing Weissenberg number in extensional flow, but slightly underestimates without regard to shear rate in shear flow. The fractional extension progresses more rapidly in extensional flow than in shear flow and the distribution of fractional extension at the formation time has a relatively sharper peak and narrower spectrum in extensional flow than in shear flow. In shear flow, the inducement of the assembly mainly results from the progress of the probability distribution of fractional extension. However, in extensional flow, the assembly is induced by both the progress of the probability distribution and increasing the values of the radial distribution.