Current Research Interests

Our current interests are in four areas (please scroll down):

  • DNA-binding proteins: We are interested in proteins that bind non-specifically to DNA and help in packaging it and reducing its volume within cells. We also determine how DNA engages with other substances outside the cell. In recent times, we have published a number of papers showing how one such protein, HU, participates in the formation of biofilms by binding to negatively-charged lipopolysaccharide on the surfaces of bacteria and helping to embed bacteria inside extracellular DNA. We have also shown that HU and another DNA packaging protein called Dps, which is made when bacterial cells are starved, undergo liquid-liquid phase separation with nucleic acids by causing their volumes to become compact and engaging in mutual crowding. This explains how bacterial DNA remains separated from the cytoplasm in prokaryotes that lack nuclear enveloped. In yet another paper, we have demonstrated how DNA packaging proteins avoid the use of the amino acid residue, tryptophan, in their sequences and structures because the presence of tryptophan serves to promote DNA oxidation through a combination of light and photosensitization, in the manner of a Trojan agent, within genomes. Similarly, we have published a few papers on the structural-functional behavior of different forms of HU and on engineered variants of HU with altered DNA packaging properties, as well as one paper showing how a fluorescently-labelled form of HU can be used to detect leaky gene expression. Work continues on our trying to understand the different roles of HU and Dps in DNA packaging within cells and biofilm formation outside bacterial cells.

  • Hyperthermophile enzymes and the degradation of plastic: We are interested in the use of enzymes to degrade plastics down to their tiniest molecular components in a manner that aids recycling. In recent times, we have published a series of papers on the degradation of polyethylene terephthalate that have achieved some of the best yields and best purities of terephthalic acid, which is the terminal degradation product of degradation. One of these uses a novel distribution of labor between two enzymes (a known enzyme and a novel enzyme) that we used synergistically to produce pure terephthalic acid in high yields from the degradation of plastic for the very first time. Two other papers demonstrate the efficacies of different protein-engineering approaches in the development of enzymes with higher activity upon plastic or higher affinity for plastic. Work continues on our trying to develop even better methods and reagents for the degradation of polyethylene terephthalate and on attempts to scale up the production of enzymes by moving from bacterial expression to fungal expression (in collaboration).

  • Hyperthermophile enzymes and the degradation of cellulosic and amylosic biomass: We are currently working on multiple fronts relating to the degradation of biomass: from bioprospecting for genes coding enzymes with novel or enhanced properties in the genomes of thermophile and hyperthermophile microbes (e.g., C. thermocellum, T. thermophilus, P. furiosus, T. onnurenius, T. maritima); to understanding how the structures of the enzymes we find, clone, and produce allow them to work efficiently so that we can make them work even better; to designing the mounting of such enzymes upon dockerin/adhesin domains to recreate minicellulosomes or mini-amylosomes to better degrade semi-crystalline biomass made of long biopolymers; to mounting such enzymes upon nanoparticles to allow them to work in synergy; to designing the best mixtures of thermostable enzymes to perform the degradation of complex (multi-component) biomass. Multiple pieces of work along these lines have been published, but many are preparatory to the development of methods that are likely to lead to technology in the future.

  • Proteins involved in cell-cell adhesions: We have been interested in proteins upon cell surfaces that are involved in cell-cell contacts and, in particular, in one class of proteins called the cadherins. We are on the verge of communicating for publication some detailed work on the behavior and characteristics of the individual domains of epithelial and neural cadherins that shed light upon how cells engage and disengage with each other.