Publications by Year: 2016

2016
C. Wang, Nguyen, P. H., Pham, K., Huynh, D., Le, T. - B. N., Wang, H., Ren, P., and Luo, R., “Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis,” Journal of computational chemistry, vol. 37, pp. 2436–2446, 2016.
D. R. Bell, Qi, R., Jing, Z., Xiang, J. Y., Mejias, C., Schnieders, M. J., Ponder, J. W., and Ren, P., “Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field,” Physical Chemistry Chemical Physics, vol. 18, pp. 30261–30269, 2016.
J. R. Houser, Busch, D. J., Bell, D. R., Li, B., Ren, P., and Stachowiak, J. C., “The impact of physiological crowding on the diffusivity of membrane bound proteins,” Soft MatterSoft Matter, vol. 12, pp. 2127-34, 2016.Abstract
Diffusion of transmembrane and peripheral membrane-bound proteins within the crowded cellular membrane environment is essential to diverse biological processes including cellular signaling, endocytosis, and motility. Nonetheless we presently lack a detailed understanding of the influence of physiological levels of crowding on membrane protein diffusion. Utilizing quantitative in vitro measurements, here we demonstrate that the diffusivities of membrane bound proteins follow a single linearly decreasing trend with increasing membrane coverage by proteins. This trend holds for homogenous protein populations across a range of protein sizes and for heterogeneous mixtures of proteins of different sizes, such that protein diffusivity is controlled by the total coverage of the surrounding membrane. These results demonstrate that steric exclusion within the crowded membrane environment can fundamentally limit the diffusive rate of proteins, regardless of their size. In cells this "speed limit" could be modulated by changes in local membrane coverage, providing a mechanism for tuning the rate of molecular interaction and assembly.
C. Narth, Lagardere, L., Polack, E., N Gresh, Q Wang,, Wang, Q., Bell, D. R., Rackers, J. A., Ponder, J. W., Ren, P. Y., and Piquemal, J. P., “Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles,” J Comput ChemJ Comput Chem, vol. 37, pp. 494-506, 2016.Abstract
We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.
Z. Ren, Jiang, S., Zeng, Q., Ding, X., Bai, S., Wang, J., Luo, Y., Su, Z., Xuan, Y., Yao, B., Cisneros, F., and Zhang, K., “Effect of dietary canthaxanthin and 25-hydroxycholecalciferol supplementation on the performance of duck breeders under two different vitamin regimens,” J Anim Sci BiotechnolJ Anim Sci Biotechnol, vol. 7, pp. 2, 2016.Abstract
BACKGROUND: Dietary canthaxanthin (CX), 25-hydroxycholecalciferol (25-OH-D 3 ) and vitamins have been widely reported to be involved in productive and reproductive performance of broiler breeders. However, limited information is available for duck breeders. In this study, a total of 1,560 Cherry Valley SM3 duck breeder females and 312 males were used to assess if the addition of CX and 25-OH-D3 could increase the performance of duck breeders under two different dietary vitamin regimens. Four diets were used under a 2 x 2 factorial arrangement with 2 kinds of vitamin premixes (REGULAR and HIGH; HIGH premix had higher levels of all vitamins except K3 than REGULAR premix), and with or without the supplementation of the mixture of CX (6 mg/kg) and 25-OH-D3 (0.069 mg/kg). The ducks were fed ad libitum with pelleted diets based on corn-soybean meal from 38 to 77 wk of age. RESULTS: HIGH vitamin premix decreased malondialdehyde (MDA) level (P < 0.001) of egg yolk, increased hatchability of fertile eggs (P = 0.029), increased hatchability of total eggs (P = 0.029), and decreased serum protein carbonyl level (P = 0.037) of breeder males. The mixture of CX and 25-OH-D3 increased serum calcium of breeder females (P = 0.010), decreased the cracked egg rate (P = 0.001), increased the pigmentation of egg yolk (P < 0.001) and male bill (P < 0.001), and decreased MDA level of egg yolk (P < 0.001) and male serum (P = 0.034). Interactive effects were observed in cracked egg rate (P = 0.038), shell thickness (P = 0.011) and serum phosphorus (P = 0.026) of breeder females. HIGH vitamin premix together with the mixture of CX and 25-OH-D3 decreased cracked egg rate and increased shell thickness of duck breeders. Serum phosphorus was decreased in duck breeder females fed REGULAR vitamin premix without the addition of the CX and 25-OH-D3 mixture. CONCLUSIONS: Dietary HIGH vitamin premix increased antioxidant status of eggs and breeder males, and increased hatchability. The mixture of CX and 25-OH-D3 enhanced egg shell quality, and promoted pigmentation and antioxidant status of eggs and breeder males.
R. Qi, Wang, Q., and Ren, P., “General van der Waals potential for common organic molecules,” Bioorg Med ChemBioorg Med Chem, vol. 24, pp. 4911-4919, 2016.Abstract
This work presents a systematic development of a new van der Waals potential (vdW2016) for common organic molecules based on symmetry-adapted perturbation theory (SAPT) energy decomposition. The Buf-14-7 function, as well as Cubic-mean and Waldman-Hagler mixing rules were chosen given their best performance among other popular potentials. A database containing 39 organic molecules and 108 dimers was utilized to derive a general set of vdW parameters, which were further validated on nucleobase stacking systems and testing organic dimers. The vdW2016 potential is anticipated to significantly improve the accuracy and transferability of new generations of force fields for organic molecules.
Q. Cui, Ren, P., and Meuwly, M., Many-Body Effects and Electrostatics in Biomolecules. Pan Stanford, 2016. Publisher's Version
T. S. Kaoud, WH Johnson, P. A., ND Ebelt, M Warthaka,, Micael Cano, S. R., Q Wang, Pengyu Ren, R. G., and Dalby, K. N., “Covalent inhibition of ERK docking interactions,” The FASEB Journal, vol. 30, no. 1, pp. 856.11-856.11, 2016.