James C. Lee, Ph.D.,
James C. Lee, Ph.D.
About the Lab
The basic normal functioning of a cell is the consequence of a delicately balanced regulation of various cellular activities. My laboratory is interested in elucidating the molecular mechanisms of regulation, in particular, the ground rules employed in recognizing specific targets and transmitting of signals among these macromolecular components. There are three biological systems being investigated.
E .coli cAMP Receptor Protein (CRP) CRP is an ideal system for elucidating the mechanism of adaptation to a change in environment. CRP regulates the expressions of 100 or more genes in E.coli whose survival depends on its ability to express proteins E. coli cAMP Receptor Protein (CRP)to transport and metabolize food sources which fluctuate. An integrated approach consisting of an integration of thermodynamics of complex formation and protein dynamics is applied to investigate CRP. As a consequence, results of our study led to a major conceptual revelation; namely, a linear correlation between protein dynamics and allosteric parameters. This implies that allosteric behavior tracks the dynamic motion of the CRP molecule. The significance of this relationship is that we have a physical property of CRP as a target, instead of a description, on an ad hoc basis, of the impact of each structural perturbation, as shown in the figure, on the functional energetics. As a consequence, we can integrate the computation and structural approaches to reveal information on protein dynamics and long range connectivity among structural elements.
West Nile Viral Envelope Protein West Nile Envelope ProteinWest Nile virus is a neurotropic flavivirus which cycles between birds and mosquitoes with humans being accidental hosts of infection. The viral envelope protein serves as both a receptor-binding and a fusion protein. Flaviviruses can be transmitted by either mosquitoes or ticks. They are associated with either encephalitic or viscerotropic diseases. Although the atomic structures of the domain 3 of the envelope proteins are very similar, we have shown that the differences in the biophysical properties of these domains correlate with biological properties of these viruses. At present we are investigating the molecular mechanism of neutralization and effect of mutations. (Structure of WNV domain 3 is kindly provided by Dr. David Volk).
Mammalian Pyruvate Kinase The PK system provides a unique opportunity to define the network of pathways involved in the allosteric regulatory of this key glycolytic enzyme. The availability of natural PK mutants of human patients suffering from PK Deficiency has identified some of the key amino acid residues. Previous studies have shown that a single amino acid mutation to the non-allosteric PK at either the Y (S402P) or Z (T340M) subunit interface can confer a certain level of allosteric regulation. In an effort to elucidate the roles of the intersubunit interaction in signal transmission and the functional structural connectivity between these interfaces, the rabbit PK mutant S402P was crystallized and its structure solved to 2.8%. The overall S402P PK structure is nearly identical to the wild type structure within experimental error. However, significant differences in the conformation of the backbone are found at the site of mutation. In addition, there is an unusual face-face interaction between the phenyl rings of Phe 25 of one chain with its counterpart of the chain across the Z interface. At the opposite end of the Z interface, there is a loss of an intersubunit salt bridge between Asp 177 and Arg 341 of the opposing subunit. Concurrent with the loss of the salt-bridge is an increase in the conformational flexibility of one of the domains which contains the active site. Comparison of previous PK structures shows a correlation between an increased movement with the loss of the Asp 177-Arg 341 salt bridge. The crystallographic and solution physical studies yield a consistent set of results to establish a functional linkage between the Y and z interfaces in regulating the interconversion of conformational states of rabbit PK. Additional studies on various mutants are on going. Results of this study will provide the necessary information to address the fundamental issue of the pathway of signal transduction in allosteric systems.
Interview with Dr. Lee
– by Jason Vertrees, 4th year BSCB Student
Dr. Lee is reclined in his high-back chair, smiling and waving me in for the interview. Upon entering Dr. Lee's office, one is quickly put at ease. You can tell from the outset that Dr. Lee likes helping students. It shows by the gifts he received from students, proudly displayed on the walls of his office. One is a large montage of student photos of the many people he's helped through the years. I sit in the chair directly beneath this montage and begin to chat with Dr. Lee.
Most BMB/BSCB students know that Dr. Lee is a cornerstone of the department/program; we just never really knew to what extent. When I asked Dr. Lee why he came to UTMB, his response, "good question." About 15 years ago, the then-chair of the BMB department, Dr. Brad Thompson, wanted to develop a biophysical chemistry department. He recruited Dr. Lee as the founding member and they went to work recruiting other faculty to round out the program. This move came with much responsbility -- Dr. Lee had to form a department/progarm on campus; what the program is now is a direct consequence of his actions starting from that time. One aspect that Dr. Lee seems proud of, concerning the Molecular Biology Educational Track, is that the program has managed to attract a diverse range of quality faculty. Their areas of research are broad and many times overlapping. This creates a smooth web of integrated science across the Molecular Biology Educational Track. It allows a student to find a lab that closely matches his or her own skillset. The last facet of the program are the students -- after the program design and recuited faculty. We students are still a major part of Dr. Lee's drive.
"To find something new, man."
–Dr. Lee, on his motivation for research.
When I asked Dr. Lee who his scientific idols were, he responded without hesitation: "Bill Jenks, Bob Ables and Serge Timasheff." Jenks and Ables, from Brandeis, were cited for how they shaped Dr. Lee's perspectives through their educational philosophy. They taught him how to think and to do useful science. Dr. Lee referred to Timasheff as a "quiet gentleman"; one who was well versed in not only science but history and other appropriate topics.
Dr. Lee shows a great tilt towards future endeavors; he maintains that his most significant scientific discovery is still just around the corner. But when he was a postdoc it his discovery of the continuum of effects of sucrose and guanidine on the stability of proteins that he sees as his most significant discovery. On a similar note, Dr. Lee couldn't point out any one scientific observation as being the best -- because their all tied together and rely on eachother, one couldn't just be singled out.
The two major goals of Dr. Lee's research are: (1) figuring out the mechanism of allostery in proteins; and (2) how viruses evade the host immune system. These two topics are currently being studied by members in his laboratory. Again smiling, Dr. Lee says it is all about "communication" in the protein.
As Dr. Lee is a well-respected faculty member on campus, I wanted to know what he thought were essential qualities of a good student. "Open mindedness, dedication, and wanting to 'know the answer'" are the qualities he thinks represent a good student. He expounded on open mindedness saying that it allows one to consider various avenues of thought and also recognize one's abilities and weaknesses.
Dr. Lee's message to all those aspiring student-scientists is: "make sure you dedicate you life to what's important." To him, it's the iterative cycle of educating the next generations that holds importance. Dr. Lee spends a huge amount of effort trying to pass on the knowledge and create active, well-educated students. The effort Dr. Lee puts forth is easily recognized and appreciated by the students; afterall, I sit underneath a montage of smiling students faces all thanking Dr. Lee for his continued drive.