1.
Perspectives on the basic and applied aspects of crassulacean acid metabolism (CAM) research.
Liu, D, Palla, KJ, Hu, R, Moseley, RC, Mendoza, C, Chen, M, Abraham, PE, Labbé, JL, Kalluri, UC, Tschaplinski, TJ, et al
Plant science : an international journal of experimental plant biology. 2018;:394-401
Abstract
Due to public concerns about the decreasing supply of blue water and increasing heat and drought stress on plant growth caused by urbanization, increasing human population and climate change, interest in crassulacean acid metabolism (CAM), a specialized type of photosynthesis enhancing water-use efficiency (WUE) and drought tolerance, has increased markedly. Significant progress has been achieved in both basic and applied research in CAM plants since the beginning of this century. Here we provide a brief overview of the current status of CAM research, and discuss future needs and opportunities in a wide range of areas including systems biology, synthetic biology, and utilization of CAM crops for human benefit, with a focus on the following aspects: 1) application of genome-editing technology and high-throughput phenotyping to functional genomics research in model CAM species and genetic improvement of CAM crops, 2) challenges for multi-scale metabolic modeling of CAM systems, 3) opportunities and new strategies for CAM pathway engineering to enhance WUE and drought tolerance in C3 (and C4) photosynthesis crops, 4) potential of CAM species as resources for food, feed, natural products, pharmaceuticals and biofuels, and 5) development of CAM crops for ecological and aesthetic benefits.
2.
Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases.
Chen, M, Kostylev, M, Bomble, YJ, Crowley, MF, Himmel, ME, Wilson, DB, Brady, JW
The journal of physical chemistry. B. 2014;(9):2306-15
Abstract
Molecular dynamics simulations were used to study the possible catalytic role of an unusual conserved water-filled pore structure in the family 48 cellulase enzyme Cel48A from Thermobifida fusca. It was hypothesized that this pore serves as the pathway for the water molecules consumed in the hydrolysis catalyzed by the enzyme to reach the active site in a continuous stream to participate in the processive reactions. Theoretical mutants of this enzyme were created in which all of the residues lining the pore were made hydrophobic, which had the effect in molecular dynamics simulations of emptying the pore of water molecules and preventing any from passing through the pore on the simulation time scale. Mutants with smaller numbers of substitutions of this nature, which could be created experimentally by site-directed mutagenesis, were also identified from simulations, and these proteins were subsequently produced in Escherichia coli, expressed and purified, but were found to not fold in a manner similar to the wild type protein, preventing the determination of the importance of the water pore for activity. It is possible that the presence of a small vacuum in the pore was responsible for the instability of the mutants. In addition, alternate pathways were observed in the simulations that would allow water molecules to reach the active site of the enzyme, suggesting that the hypothesis that the pore has functional significance might be incorrect.
3.
Size effect on nucleation rate for homogeneous crystallization of nanoscale water film.
Lü, Y, Zhang, X, Chen, M
The journal of physical chemistry. B. 2013;(35):10241-9
Abstract
The nucleation rate from classical nucleation theory is independent of sample size. In the past decades, several experimental and theoretical studies argued that the homogeneous nucleation rate of ice in supercooled droplets increases when the drop size is decreased. In this paper, we investigate the nucleation of ice in nanoscale water films using molecular dynamics simulations. We found that the nucleation rate of ice actually decreases when the film thickness decreases in the nanoscale regime. A theoretical model is presented to interpret the mechanism of nucleation rate decrease, which agrees well with the simulation results. The model divides films into the near-surface and the middle regions that are characterized by relatively low and high nucleation rates, respectively. The middle region dominates the nucleation process of films, whereas its effect is continuously weakened when increasing volume fraction of the near-surface region by decreasing the film size, leading to a decrease of the total nucleation rate. The structural and thermodynamic analyses indicate that the high stress induced by the surface layering slows down the diffusion and increases the nucleation barrier in the near-surface region, which is responsible for the low nucleation rate and eventually the decrease of the total nucleation rate.
4.
Weakly hydrated surfaces and the binding interactions of small biological solutes.
Brady, JW, Tavagnacco, L, Ehrlich, L, Chen, M, Schnupf, U, Himmel, ME, Saboungi, ML, Cesàro, A
European biophysics journal : EBJ. 2012;(4):369-77
Abstract
Extended planar hydrophobic surfaces, such as are found in the side chains of the amino acids histidine, phenylalanine, tyrosine, and tryptophan, exhibit an affinity for the weakly hydrated faces of glucopyranose. In addition, molecular species such as these, including indole, caffeine, and imidazole, exhibit a weak tendency to pair together by hydrophobic stacking in aqueous solution. These interactions can be partially understood in terms of recent models for the hydration of extended hydrophobic faces and should provide insight into the architecture of sugar-binding sites in proteins.