Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.

A hypothesis for insulin resistance in primary human adipocytes involving MRTF-A and suppression of PPARγ.

Obesity is the main risk factor behind insulin resistance and type 2 diabetes. Still, the mechanism behind adipocyte dysfunction is not yet resolved. Recently, we reported that rapid actin remodeling correlates with adipose cell size changes after short-term overfeeding. Therefore, we hypothesized that the actin-driven myocardin-related transcription factor (MRTF-A) contributes to impaired mature adipocyte function. Primary human adipocytes were subjected to adenoviral overexpression of MRTF-A or MRTF-B, followed by Western blot analysis and tracer glucose uptake assay. Further, we assessed cell size distribution, insulin response, MRTF-A localization, actin organization and degree of polymerization in adipocytes isolated from Ob/Ob mice. Overexpression of MRTF-A, but not MRTF-B, markedly suppressed PPARγ expression. Further, MRTF-A expression resulted in decreased IRS-1 level, shifted phosphorylation of Akt (pS473/pT308), IRS-1 (pS302) and AS160 (pT642), and lowered insulin-stimulated glucose uptake. Hypertrophic adipocytes from Ob/Ob mice displayed an increased proportion of polymerized actin, and increased nuclear translocation of MRTF-A compared with control (Ob/+). Similar with human adipocytes overexpressing MRTF-A, adipocytes isolated from Ob/Ob mice had reduced expression of IRS-1 and PPARγ, as well as impaired insulin response. Together, these data demonstrate that MRTF-A negatively influences insulin sensitivity and the expression of key targets in fully mature human adipocytes. This suggests that MRTF-A is poised to exert a transcriptional response in hypertrophic adipocytes, contributing to adipocyte dysfunction and insulin resistance.

ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field.

We have implemented the Martini force field within Lawrence Livermore National Laboratory's molecular dynamics program, ddcMD. The program is extended to a heterogeneous programming model so that it can exploit graphics processing unit (GPU) accelerators. In addition to the Martini force field being ported to the GPU, the entire integration step, including thermostat, barostat, and constraint solver, is ported as well, which speeds up the simulations to 278-fold using one GPU vs one central processing unit (CPU) core. A benchmark study is performed with several test cases, comparing ddcMD and GROMACS Martini simulations. The average performance of ddcMD for a protein-lipid simulation system of 136k particles achieves 1.04 µs/day on one NVIDIA V100 GPU and aggregates 6.19 µs/day on one Summit node with six GPUs. The GPU implementation in ddcMD offloads all computations to the GPU and only requires one CPU core per simulation to manage the inputs and outputs, freeing up remaining CPU resources on the compute node for alternative tasks often required in complex simulation campaigns. The ddcMD code has been made open source and is available on GitHub at https://github.com/LLNL/ddcMD.

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

Impaired glucose transport in inguinal adipocytes after short-term high-sucrose feeding in mice.

Diets enriched in sucrose severely impair metabolic regulation and are associated with obesity, insulin resistance and glucose intolerance. In the current study, we investigated the effect of 4 weeks high-sucrose diet (HSD) feeding in C57BL6/J mice, with specific focus on adipocyte function. Mice fed HSD had slightly increased adipose tissue mass but displayed similar hepatic triglycerides, glucose and insulin levels, and glucose clearance capacity as chow-fed mice. Interestingly, we found adipose depot-specific differences, where both the non- and insulin-stimulated glucose transports were markedly impaired in primary adipocytes isolated from the inguinal fat depot from HSD-fed mice. This was accompanied by decreased protein levels of both GLUT4 and AS160. A similar but much less pronounced trend was observed in the retroperitoneal depot. In contrast, both GLUT4 expression and insulin-stimulated glucose uptake were preserved in adipocytes isolated from epididymal adipose tissue with HSD. Further, we found a slight shift in cell size distribution towards larger cells with HSD and a significant decrease of ACC and PGC-1α expression in the inguinal adipose tissue depot. Moreover, fructose alone was sufficient to decrease GLUT4 expression in cultured, mature adipocytes. Altogether, we demonstrate that short-term HSD feeding has deleterious impact on insulin response and glucose transport in the inguinal adipose tissue depot, specifically. These changes occur before the onset of systemic glucose dysmetabolism and therefore could provide a mechanistic link to overall impaired energy metabolism reported after prolonged HSD feeding, alone or in combination with HFD.

An Ab Initio Exciton Model Including Charge-Transfer Excited States.

The Frenkel exciton model is a useful tool for theoretical studies of multichromophore systems. We recently showed that the exciton model could be used to coarse-grain electronic structure in multichromophoric systems, focusing on singly excited exciton states [ Acc. Chem. Res. 2014 , 47 , 2857 - 2866 ]. However, our previous implementation excluded charge-transfer excited states, which can play an important role in light-harvesting systems and near-infrared optoelectronic materials. Recent studies have also emphasized the significance of charge-transfer in singlet fission, which mediates the coupling between the locally excited states and the multiexcitonic states. In this work, we report on an ab initio exciton model that incorporates charge-transfer excited states and demonstrate that the model provides correct charge-transfer excitation energies and asymptotic behavior. Comparison with TDDFT and EOM-CC2 calculations shows that our exciton model is robust with respect to system size, screening parameter, and different density functionals. Inclusion of charge-transfer excited states makes the exciton model more useful for studies of singly excited states and provides a starting point for future construction of a model that also includes double-exciton states.

Characterization of the Azirinyl Cation and Its Isomers.

The azirinyl cation (C2H2N(+)) and its geometrical isomers could be present in the interstellar medium. The C2H2N(+) isomers are, however, difficult to identify in interstellar chemistry because of the lack of high-resolution spectroscopic data from laboratory experiments. Ab initio quantum chemical methods were used to characterize the structures, relative energies, and spectroscopic and physical properties of the low energy isomers of the azirinyl cation. We have employed second-order Møller-Plesset perturbation theory (MP2), second-order Z-averaged perturbation theory (ZAPT2), and coupled cluster theory with singles and doubles with perturbative triples CCSD(T) methods along with large correlation consistent basis sets such as cc-pVTZ, cc-pCVTZ, cc-pVQZ, cc-pCVQZ, and cc-pV5Z. Harmonic vibrational frequencies, dipole moments, rotational constants, and proton affinities for the lowest energy isomers were calculated using the CCSD(T) method. Azirinyl cation, a cyclic isomer, is lowest in energy at all levels of theory employed. Azirinyl cation is followed by the cyanomethyl cation (H2CCN)(+), isocyanomethyl cation (H2CNC)(+), and a quasilinear HCCNH(+) cation, which are 13.8, 17.3, and 21.5 kcal mol(-1) above the cyclic isomer, respectively, at the CCSD(T)/cc-pV5Z level of theory. The lowest three isomers all have C2v symmetry and (1)A1 ground electronic states. The quasilinear HCCNH(+) cation has a Cs symmetry planar structure, and a (3)A″ electronic ground state, unlike what some previous work suggested.

Tensor Hypercontraction Second-Order Møller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies.

We have recently introduced the tensor hypercontraction (THC) method for electronic structure, including MP2. Here, we present an algorithm for THC-MP2 that lowers the memory requirements as well as the prefactor while maintaining the formal quartic scaling that we demonstrated previously. We also describe a procedure to optimize quadrature grids used in grid-based least-squares (LS) THC-MP2. We apply this algorithm to generate grids for first-row atoms with less than 100 points/atom while incurring negligible errors in the computed energies. We benchmark the LS-THC-MP2 method using optimized grids for a wide variety of tests sets including conformational energies and reaction barriers in both the cc-pVDZ and cc-pVTZ basis sets. These tests demonstrate that the THC methodology is not limited to small basis sets and that it incurs negligible errors in both absolute and relative energies.

Vitamin C supplementation slightly improves physical activity levels and reduces cold incidence in men with marginal vitamin C status: a randomized controlled trial.

The early indications of vitamin C deficiency are unremarkable (fatigue, malaise, depression) and may manifest as a reduced desire to be physically active; moreover, hypovitaminosis C may be associated with increased cold duration and severity. This study examined the impact of vitamin C on physical activity and respiratory tract infections during the peak of the cold season. Healthy non-smoking adult men (18-35 years; BMI < 34 kg/m2; plasma vitamin C < 45 µmol/L) received either 1000 mg of vitamin C daily (n = 15) or placebo (n = 13) in a randomized, double-blind, eight-week trial. All participants completed the Wisconsin Upper Respiratory Symptom Survey-21 daily and the Godin Leisure-Time Exercise Questionnaire weekly. In the final two weeks of the trial, the physical activity score rose modestly for the vitamin C group vs. placebo after adjusting for baseline values: +39.6% (95% CI [-4.5,83.7]; p = 0.10). The number of participants reporting cold episodes was 7 and 11 for the vitamin C and placebo groups respectively during the eight-week trial (RR = 0.55; 95% CI [0.33,0.94]; p = 0.04) and cold duration was reduced 59% in the vitamin C versus placebo groups (-3.2 days; 95% CI [-7.0,0.6]; p = 0.06). These data suggest measurable health advantages associated with vitamin C supplementation in a population with adequate-to-low vitamin C status.