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All Publications

  • Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. The ISME journal Li, P. N., Herrmann, J., Tolar, B. B., Poitevin, F., Ramdasi, R., Bargar, J. R., Stahl, D. A., Jensen, G. J., Francis, C. A., Wakatsuki, S., van den Bedem, H. 2018


    Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH4+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH4+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH4+ availability, with broad implications for comparisons of ecologically distinct populations.

    View details for PubMedID 29899515

  • Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer BIOPHYSICAL JOURNAL Herrmann, J., Jabbarpour, F., Bargar, P. G., Nomellini, J. F., Li, P., Lane, T. J., Weiss, T. M., Smit, J., Shapiro, L., Wakatsuki, S. 2017; 112 (9): 1841-1851


    Surface layers (S-layers) are paracrystalline, proteinaceous structures found in most archaea and many bacteria. Often the outermost cell envelope component, S-layers serve diverse functions including aiding pathogenicity and protecting against predators. We report that the S-layer of Caulobacter crescentus exhibits calcium-mediated structural plasticity, switching irreversibly between an amorphous aggregate state and the crystalline state. This finding invalidates the common assumption that S-layers serve only as static wall-like structures. In vitro, the Caulobacter S-layer protein, RsaA, enters the aggregate state at physiological temperatures and low divalent calcium ion concentrations. At higher concentrations, calcium ions stabilize monomeric RsaA, which can then transition to the two-dimensional crystalline state. Caulobacter requires micromolar concentrations of calcium for normal growth and development. Without an S-layer, Caulobacter is even more sensitive to changes in environmental calcium concentration. Therefore, this structurally dynamic S-layer responds to environmental conditions as an ion sensor and protects Caulobacter from calcium deficiency stress, a unique mechanism of bacterial adaptation. These findings provide a biochemical and physiological basis for RsaA's calcium-binding behavior, which extends far beyond calcium's commonly accepted role in aiding S-layer biogenesis or oligomerization and demonstrates a connection to cellular fitness.

    View details for DOI 10.1016/j.bpj.2017.04.003

    View details for Web of Science ID 000401301600013

    View details for PubMedID 28494955

  • Determination of three-dimensional atomic positions from tomographic reconstruction using ensemble empirical mode decomposition NEW JOURNAL OF PHYSICS Li, P., Wu, Z., Hsiao, C., Lee, T., Chen, C. 2016; 18
  • Method to enhance the resolution of x-ray coherent diffraction imaging for non-crystalline bio-samples NEW JOURNAL OF PHYSICS Lan, T., Li, P., Lee, T. 2014; 16
  • Subwavelength localization of near fields in coupled metallic spheres for single-emitter polarization analysis Opt. Lett. Li, P., Tsao, H., Huang, J., Huang, C. 2011; 36 (12): 2339

    View details for DOI 10.1364/OL.36.002339