Department of Biochemistry and Molecular Biology
EDUCATION AND APPOINTMENTS
Baylor University, Waco, TX, B.S. Chemistry, 1990
University of Iowa, Iowa City, Ph.D., Biochemistry, 1995
W.M. Keck Center for Computational Biology, Postdoctoral Fellow, 1995-99
Rice University, Biochemistry & Cell Biology Robert A. Welch Postdoctoral Fellow, 2000-2002
Rice University, Biochemistry & Cell Biology, Research Scientist, 2002-2004
University of Kansas Medical Center, Assistant Professor, Biochemistry and Molecular Biology, 2004 - 2009
University of Kansas Medical Center, Associate Professor, Biochemistry and Molecular Biology, 2009 - present
University of Kansas - Lawrence, Associate Professor, Molecular Biosciences, Courtesy Appointment, 2009 - present
University of Kansas Medical Center, Director of Graduate Studies, Biochemistry and Molecular Biology, 2009 - present
Publications: Click here
Major Research Interest
In sequence alignments of protein families, amino acid residues fall into three groups. Conserved residues convey a common function (e.g. DNA-binding). Nonconserved residues either fine-tune the distinct functions of homologous family members (e.g. recognition of different DNA sequences) or are “silent” (mutagenesis has no impact).
Understanding the link between amino acid variation of nonconserved residues and variation in protein function is important for protein engineering and individualized patient therapies. These applications are impeded by difficulties in discriminating important nonconserved residues from silent residues. To differentiate these groups, myriad bioinformatics algorithms have been recently developed. The algorithms rely upon the untested assumption that a given site falls into a given group for every homologue. Further, the algorithms cannot predict which aspect of function is altered by each nonconserved position. For example, amino acid variation in a transcription repressor might alter affinity or selectivity for DNA or allosteric response to regulatory ligand.
My research bridges bioinformatics, biochemistry, and biophysics to identify important nonconserved residues. Using transcription repressors, we characterize in vivo function of multiple variants for multiple homologues. Chimeric proteins are used to simultaneously facilitate comparisons between homologues and to investigate contributions from residues that do not directly contact DNA. Results from mutagenesis test predicted locations, discover trends among homologues, and suggest improved strategies for sequence analyses. Biophysical experiments delineate which aspect of function is linked to each nonconserved residue and determine whether these roles are conserved among homologues. Future studies will extend to other protein families.
EXPERIMENTAL: One of the common approaches to protein engineering is to recombine domains and thus create novel combinations of functions. However, if the domain-domain interface contains specificity determinants, the new protein could have unanticipated functional properties. We are identifying the specificity determinants that are present in the interface between the DNA-binding and regulatory domains of the LacI/GalR proteins. Our general strategy is to exchange domains between family members and use tools from biology and biochemistry to identify which positions convey various unique functions to individual proteins. Results will be used to develop rules for reliably recombining domains in this family and to evaluate and improve bioinformatics analyses of protein families in general.
COMPUTATIONAL: The regulatory domains of LacI/GalR transcription control proteins are also structurally homologous to the periplasmic binding proteins and extracellular domains of some G-protein coupled receptors. All of these families are involved in signaling processes and utilize the same general strategy - bind a small molecule in a central cleft and propagate the message to another part of the protein. Differences between the proteins include: (1) The small molecule signal is different for each protein. (2) The signaling pathways through the protein structure as well as the final molecular location of the information differs both within and between the protein families. Targeted molecular dynamics (TMD) is being used to simulate motions in the proteins as the message is propagated from the binding site to other regions of the protein. Data from homologues will be compared and contrasted to identify the range of signaling pathways supported by the common underlying protein fold. Ultimately, we will use this information to construct homologues with novel signaling functions.
Liskin Swint-Kruse, Ph.D.