Faculty
Alfonso Mondragón
Professor
Molecular Biosciences
PhD, University of Cambridge
Email: a-mondragon@northwestern.edu
Phone: (847) 491-7726
Fax: (847) 467-1380
Room: Cook 4131
Research Interests
Our laboratory is interested in three main areas: DNA topoisomerases, catalytic RNA molecules, and the molecular basis of spectrin flexibility.
DNA topoisomerases. The long term goal of our
work is to understand the catalytic mechanism of these molecules
in atomic detail. In particular, we are interested in understanding
how these enzymes perform complex topological rearrangements of DNA
molecules. DNA topoisomerases are of interest for several reasons:
1) they are responsible for maintaining the topological state of
DNA and are involved in a variety of crucial cellular processes.
2) Their involvement in key processes has lead to the development
of drugs whose target is topoisomerases. 3) Topoisomerases catalyze
a complex reaction that involves cutting and resealing the DNA and
passing DNA strands through this break. These reactions are not easy
to visualize or understand. The structures of several topoisomerases
and fragments of them have truly led to a near-atomic picture of
the way a very complex reaction is catalyzed. 4) Topoisomerases are
excellent examples of complex molecular machines that perform a complicated
reaction in the cell. Type I enzymes work in the absence of an external
energy source, such as ATP, and for this reason present an opportunity
to understand a process where the energy to drive large domain movements
is harnessed from the energy stored in the DNA, and 5) The structural
studies may provide the information to develop new chemotherapeutic
agents.
In
the last few years our laboratory has worked on the structure of
several different type I topoisomerases, including E. coli DNA
topoisomerases I and III (type IA), and vaccinia virus and Deinococcus
radiodurans topoisomerase I (type IB), and more recently
on Methanopyrus kandleri topoisomerase V. In all cases,
a combination of structural and biochemical work has helped elucidate
the atomic basis of the catalytic mechanism of these enzymes.
Catalytic RNA molecules. A
second large research area is the structure of large RNA molecules
and, in particular, RNase P. RNA plays a pivotal role in biology
as it is involved in many cellular processes. It is also unique amongst
nucleic acids in being able to perform chemical catalysis. In the
cell, RNA molecules can self-cleave or process other RNA molecules
in a manner that up to a few years ago was completely unknown and
unexpected. These findings have led to the idea of a pre-biotic RNA-world,
where RNA molecules were the first molecules to appear. The discovery
of the catalytic properties of RNA molecules has also rekindled the
interest in these molecules both from a basic and from an applied
point of view.
RNase
P is one of only two ribozymes conserved in all three kingdoms of
life and is required in the 5' maturation of all tRNAs. In the last
years, we solved the crystal structures of the specificity domain
of Bacillus subtilis and Thermus thermophilus RNase
P and also of the intact RNA component of T. maritima RNase
P. In the structure of the intact molecule, the entire RNA catalytic
component is revealed, as well as the arrangement of the two structural
domains. The structure shows the general architecture of the RNA
molecule, the inter- and intra-domain interactions, the location
of the universally conserved regions, the regions involved in pre-tRNA
recognition, and the location of the active site. A model with bound
tRNA is in excellent agreement with all existing data and suggests
the general basis for RNA-RNA recognition by this ribozyme. This
is the first structure of an A-type bacterial RNase P solved and
represents one of the largest RNA molecules whose structure is known.
In
the future we plan to continue our work on RNase P. Our immediate
goals are to obtain structures of the holoenzyme and a tertiary complex
involving the RNA component, the protein component, and pre-tRNA.
Spectrin. Proteins
of the spectrin superfamily are designed for the vital task of providing
cells with a deformable skeleton and a flexible matrix. Members
of this ubiquitous family, such as a-spectrin and dystrophin, are
long molecules formed by tandem repeating units of 106-109 amino
acids, each folded into a triple-helical coiled-coil. Understanding
of the relative arrangement of the repeats, the nature of the linker
region between them, and the general disposition of the repeats is
crucial to further our knowledge of spectrin flexibility. To
address these questions, we solved the structure of several related
molecules formed by two or three repeats of a-spectrin. The
structures show that spectrin has an ordered a-helical linker region,
that the relative arrangements of the repeats can vary, and that
the repeats can rearrange themselves. The structures allowed
us to propose two possible models for spectrin flexibility, the first
models based on atomic data.
We are now also focusing our attention on repeats of human spectrin that contain the region involved in interactions with other cytoskeletal proteins such as ankyrin. We are employing a combination of biophysical and structural approaches with the long term goal of understanding the atomic basis of the interaction of spectrin and other cellular proteins.
Selected Publications
Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways. Terekhova K, Gunn KH, Marko JF, and Mondragón A. Nucleic Acids Research. 2012 November;40(20):10432-10440.
The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning. Reiter NJ, Osterman AK, and Mondragón A. Nucleic Acids Research. 2012 November;40(20):10384-10393.
Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin. Yasunaga M, Ipsaro JJ, and Mondragón A. Journal of Molecular Biology. 2012 April 6;417(4):336-350.
Emerging structural themes in large RNA molecules. Reiter NJ, Chan CW, and Mondragón A. Current Opinion in Structural Biology. 2011 June;21(3):319-326.
Preference by Exclusion. Godley LA and Mondragón A. Science. 2011 February 25;331(6020):1017-1018.
Solution structures of DNA-bound gyrase. Baker NM, Weigand S, Maar-Mathias S, and Mondragón A. Nucleic Acids Research. 2011 January;39(2):755-766.
Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, and Mondragón A. Nature. 2010 December 9;468(7325):784-789.
Structures of Minimal Catalytic Fragments of Topoisomerase V Reveals Conformational Changes Relevant for DNA Binding. Rajan R, Taneja B, and Mondragón A. Structure. 2010 July 14;18(7):829-838.
Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex. Ipsaro JJ, Harper SL, Messick TE, Marmorstein R, Mondragón A, and Speicher DW. Blood. 2010 June 10;115(23):4843-4852.
Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site. Patel A, Yakovleva L, Shuman S, and Mondragón A. Structure. 2010 June 9;18(6):725-733.
View all publications by Alfonso Mondragón listed in the National Library of Medicine (PubMed). Current and former IBiS students in blue.