Wlodek M. Bujalowski, PhD,
Professor
- Affiliations: Affiliations: Department of Biochemistry & Molecular Biology; Professor, Sealy Center for Structural Biology; Department of Obstetrics and Gynecology; Member, Sealy Center for Cancer Cell Biology
- Tel: (409) 772-5634
- Fax: (409) 772-1790
- wbuajalow@utmb.edu
- Route: 1053; 5.138D MRBDepartment of Biophysical, Structural, & Computational Biology
- Dr. Bujalowski's Publications
- Dr. Bujalowski's Lab
Wlodek M. Bujalowski, PhD
About the Lab
Great interest in the mechanism by which proteins interact with nucleic acids results from the extreme importance of these interactions for many vital cellular processes including replication, recombination, repair, transcription and translation. We have a long-term interest in quantitative understanding of the structure-function relationships in protein-nucleic acid interactions in solution. Such understanding can be achieved through rigorous thermodynamic, kinetic, and structural (spectroscopic) studies of both macromolecules and their relevant complexes. The current major projects in our laboratory focus on: 1. Quantitative molecular understanding of the mechanism of a replicative helicase. 2. Quantitative determination of the mechanism of DNA substrate recognition by a DNA polymerase. Both helicases and polymerases are two classes of essential enzymes involved in DNA metabolism.
Part of our work is directed toward development novel rigorous quantitative methods to study thermodynamics and kinetics of complex macromolecular interactions in solution using powerful spectroscopic techniques which include steady-state and life-time fluorescence spectroscopy, fluorescence energy transfer and anisotropy techniques, analytical ultracentrifugation, dynamic light scattering, fast chemical kinetics, and various other biochemical methods.
I. HELICASES
Single-stranded DNA is a crucial intermediate in the course of DNA replication, recombination, and repair. These processes are fundamental for the transmission of genetic information. Thus, these processes require that duplex DNA is, at least transiently, unwound to form a single-stranded conformation. The unwinding reaction, possibly a rate limiting step for replication, recombination, and repair, is catalyzed by a class of enzymes called helicases. Helicases belong to a group of motor proteins which perform vectorial processes fueled by transduction of the free energy of NTP hydrolysis into a catalyzed reaction. Determination of the helicase mechanism will provide invaluable information as to how these remarkable biological machines couple the binding and hydrolysis of nucleotide triphosphates to another reaction, allowing the enzymes to perform efficient catalysis against a gradient of the chemical potential or the mechanical stress. As a primary replicative helicase in E. coli, the DnaB protein provides an outstanding model system to study the molecular mechanism of the helicase action. Our laboratory is currently examining the mechanism of the functioning of the hexameric DnaB helicase, through quantitative studies of the thermodynamics, kinetics, and structure of its complexes with nucleic acids and nucleotide cofactors. Other helicases, including the E. coliPriA protein are also quantitatively examined.
II. DNA REPAIR POLYMERASES
Transmission of genetic information from one generation of cells to another, as well as repair of damaged DNA, relies on the correct replication of the cellular DNA. DNA replication is a very complex process in which the dsDNA is unwound and the two resultant single strands of the nucleic acid act as templates to guide the synthesis, one nucleotide at a time, on antiparallel primer strands. At the core of DNA replication is the nucleotidyl transfer reaction catalyzed by highly specific enzymes, DNA polymerases. Polymerase b is one of several recognized DNA-directed polymerases of the eukaryotic nucleus. The enzyme plays a very specialized function in the DNA repair machinery in mammalian cells. Pol b conducts "gapped-filling" synthesis in a processive fashion in mismatch repair, in the repair of monofunctional adducts, UV damaged DNA, and abasic lesions in the nucleic acid. Our major interest is to elucidate the mechanism of the DNA substrate recognition by the pol b through the examination of the thermodynamics, kinetics, and structure of the enzyme complexes with the template-primer, gapped DNA, and nucleotide cofactors.
Interview with Dr. Bujalowski
– by Austin Elam, 2nd year BSCB Student
Dr. Wlodek M. Bujalowski was first drawn to the University of Texas-Medical Branch (UTMB) in 1989 by the prospect of building a strong biophysical and structural biology program. He and Dr. James Lee are the two original faculty members of the biophysical, computational, and structural biology (BSCB) program. Dr. Bujalowski enjoys being part of the BSCB program because it brings together motivated and “quantitatively-minded” students with some of the best faculty in this area of expertise.
As a professor who has a strong interest in the history of science, Dr. Bujalowski has many scientific idols such as Newton, Schrödinger, and Einstein. Importantly, he admires their passion and motivation that these famous individuals exhibited in their pursuit of science. When asked what motivates him to do research, Dr. Bujalowski indicated that simple curiosity about the surrounding world was one of his main driving forces. Regarding human understanding of molecular biochemistry, he elaborates saying, “I’m frankly amazed that we can actually understand how things work. We’re getting something right.”
When asked what he thought was the most profound achievement in all of science, Dr. Bujalowski smiled. After a few minutes of thought, he stated, “Copernican Revolution (heliocentric theory) is probably one of the most significant scientific achievements in human history because it changed man’s perspective forever. Further, it set the stage for the period of the Enlightenment which followed soon after.”
While working with Manfred Eigen (Nobel Laureate) at the Max-Planck Institute in Gottingen, Germany, Dr. Bujalowski made several significant scientific observations which set foundations for study of codon/anticodon interaction and replicative adaptation. He has also contributed to the discovery of different binding modes of DNA polymerases. Currently, Dr. Bujalowski’s interests are in understanding the correlation between structure of proteins such and DNA helicases and polymerases and their function. Importantly, he uses comprehensive approaches including kinetic studies, thermodynamics, structural analysis and spectroscopy to better understand how molecular structures are involved in molecular interactions and function. In the near future, he hopes to develop a complete understanding of energetics of catalysis of nucleotide hydrolysis, a process which provides energy for DNA unwinding and synthesis.
Dr. Bujalowski believes that the two qualities most important for graduate students are motivation and persistence. Regarding the ability of graduate students to learn difficult scientific ideas, he said, “There is nothing created by another person that you should not be able to understand”. Concerning the satisfaction and excitement of working in science, he simply said, “Science is a demanding but enjoyable life, and, on lighter note, whatever you learn is yours to keep.”