Multiscale Geometric Modeling of Macromolecules I: Cartesian Representation

This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace–Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the polarized curvature, for the prediction of protein binding sites

Iron(III) Chloride-catalyzed Nucleophilic Substitution of Propargylic Alcohols: A General and Efficient Approach for the Synthesis of 1,4-Diynes

A wide variety of 1,4-diynes have been constructed via a novel FeCl(3)-catalyzed coupling reaction of propargylic alcohols with alkynylsilanes. This synthetic approach provides a general, efficient, and economical route to 1,4-cliynes.National Natural Science Foundation of China[20772098, 21072159

Study on the Variation of Terrestrial Water Storage and the Identification of Its Relationship with Hydrological Cycle Factors in the Tarim River Basin, China

The terrestrial water storage anomalies (TWSAs) in the Tarim River Basin (TRB) were investigated and the related factors of water variations in the mountain areas were analyzed based on Gravity Recovery and Climate Experiment (GRACE) data, in situ river discharge, and precipitation during the period of 2002–2015. The results showed that three obvious flood events in 2005, 2006, and 2010 resulted in significant water surplus, although TWSA decreased in the TRB during 2002–2015. However, while the significant water deficits in 2004, 2009, and 2011 were associated with obvious negative river discharge anomalies at the hydrological stations, the significant water deficits were not well consistent with the negative anomalies of precipitation. While the river discharge behaved with low correlations with TWSA, linear relationships between TWSA and climate indices were insignificant in the TRB from 2002 to 2015. The closest relationship was found between TWSA and Pacific Decadal Oscillation (PDO), with correlations of -0.56 and 0.58 during January 2010–December 2015 and during January 2006–December 2009, respectively. Meanwhile, the correlation coefficient between TWSA and El Niño-Southern Oscillation (ENSO) index in the period of April 2002–December 2005 was -0.25, which reached the significant level (p<0.05)

Meniscus confined fabrication of multidimensional conducting polymer nanostructures with scanning electrochemical cell microscopy (SECCM)

Scanning electrochemical cell microscopy (SECCM) is demonstrated as a new approach for the construction of extended multi-dimensional conducting polymer (polyaniline) nanostructures, making use of a mobile dual-channel theta pipette cell to control and monitor the location, rate and extent of electropolymerisation

A novel auxiliary subunit critical to BK channel function in caenorhabditis elegans

The BK channel is a Ca(2+)- and voltage-gated potassium channel with many important physiological functions. To identify proteins important to its function in vivo, we screened for C. elegans mutants that suppressed a lethargic phenotype caused by expressing a gain-of-function (gf) isoform of the BK channel α-subunit SLO-1. BKIP-1, a small peptide with no significant homology to any previously characterized molecules was thus identified. BKIP-1 and SLO-1 showed similar expression and subcellular localization patterns, and appeared to interact physically through discrete domains. bkip-1 loss-of-function (lf) mutants phenocopied slo-1(lf) mutants in behavior and synaptic transmission, and suppressed the lethargy, egg-laying defect, and deficient neurotransmitter release caused by SLO-1(gf). In heterologous expression systems, BKIP-1 decreased the activation rate and shifted the conductance-voltage (G-V) relationship of SLO-1 in a Ca(2+)-dependent manner, and increased SLO-1 surface expression. Thus, BKIP-1 is a novel auxiliary subunit critical to SLO-1 function in vivo