Friday Funnies

It's the last Friday of the month! To celebrate, I thought I would supply some humor.

When I Read An Article Outside Of My Discipline

Thiostrepton tryptophan methyltransferase (TsrM)

Methylation is a common modification that occurs on both nucleic and amino acids, and plays an important role in the function of biomolecules. The enzymes responsible for performing this methylation are called methyltransferases (MTase; E.C. 2.1) In many cases, MTases utilize the co-factor S-adenosylmethionine (SAM) as their source of methyl. In canonical methylation chemistry, the electrophilic methyl group reacts with a nucleophilic substrate to give the final product. These reactions typically occur with an inversion of stereochemistry (SN2), and are frequently seen on carbon, nitrogen or oxygen nucleophiles (1).

A growing class of enzymes, the radical SAM family, utilize SAM in a different manner. These enzymes are able to cleave SAM reductively and use the resultant 5'-deoxyadenosyl radical intermediate to perform a wide range of ususual chemical reactions, including cofactor biosynthesis, peptide modifications, and lipid metabolism (1, 2). Radical SAM enzymes are present in all domains of life, and share a conserved CxxxCxxC motif to coordinate an iron-sulfur cluster necessary to perform the radical chemistry (1). 

Radical SAM enzymes can be divided into 3 classes based on their sequence homology. However I'm going to focus on those in Class B, which contain both the conserved CxxxCxxC motif and a cobalamin-binding domain. There has been growing interest in the radical SAM community over the methyltransferase TsrM (a member of Class B) because of its unique mechanism of action. Recently, a report on TsrM by Pierre et al. appeared in Nature Chemical Biology (3).

TsrM is involved in the biosynthetic pathway of Thiostrepton A, a thiopeptide antibiotic that undergoes numerous post-translational modifications. TsrM contains a cobalamin co-factor and was hypothesized to methylate tryptophan to 2-methyltryptophan. This methylated tryptophan ultimately serves as a precursor to the quinaldic acid moiety in the antibiotic. In their study, Pierre et al. cloned and overexpressed TsrM in E. coli and characterized its activity in vitro.

Initial experiments confirmed the necessity of methylcobalamin during the reaction. Interestingly, while 2-methyltryptophan production is coupled to SAH, there was no observation 5'-deoxyadeonise (5'dA). The presence of 5'dA would suggest the formation of a 5'-deoxyadenosyl radical as an intermediate during the reaction. Because none of this product was observed, this suggests that SAM does not undergo homolytic cleavage, but is used only as a source of methyl (3).

Interestingly, when (methyl-d3)-SAM was used in labeling experiments, the product was exclusively (methyl-d3)-2-methyladenosine, even in the presence of excess unlabeled methylcob(III)lamin. This suggests that the enzyme binds free cobalamin, which is then methylated by SAM after it is bound. To further elucidate the mechanism, the authors performed UV-Vis spectroscopy to identify key cobalamin intermediate species. Spectroscopy was able to detect Co(II) and Co(III). Yet in contrast to other cobalamin-dependent enzymes, no formation of Co(I) was observed. However in the proposed mechanism, it was suggested that Co(II) is converted to Co(I) with help from the [4Fe-4S] cluster (3). 

Proposed Mechanism of TsrM (2,3):

While some questions remain, continued work on the mechanism of this enzyme, as well as other radical SAMs is expected to shed light on this unique methylation. As genomics efforts continue to identify novel gene clusters, it is likely that more fascinating radical SAM chemistry will soon be discovered.

References:
1. Zhang et al. "Radical-Mediated Enzymatic Methylation: A Tale of Two SAMs." Accounts Chem. Res. 2011, 45, 555-564.
2. Chan, et al. "The Mechanisms of Radical SAM/Cobalamin Methylations: An Evolving Working Hypothesis." ChemBioChem, 2013, doi: 10.1002/cbic.201200762
3. Pierre et al. "Thiostrepton tryptophan methyltransferase expands the chemistry of radical SAM enzymes." Nat. Chem. Biol., 2012, 8, 957-959. doi: 10.1038/nchembio.1091

Chemical Biology vs. Biological Chemistry

"What is chemical biology and how is that different from biochemistry?"

This is the one question I am often asked at family functions, by other students, and sometimes even by other chemists who are not familiar with the discipline. The answer: it’s complicated!

If you search for "chemical biology" on the internet, the results would include hundreds of websites, college syllabi, and opinion pieces, each attempting to describe the field or explain the methodology used by researchers. And while there are some excellent resources about this field, many more results simply describe the idea that chemical biology is “something chemical” associated with “something biological” (1).

Even the experts, those researchers pushing the frontiers of the field, have difficulty nailing down a unified description of what constitutes chemical biology--some arguing that is is the techniques being utilized while others arguing that it is the type of questions being asked. Personally, I like Christopher Walsh's definition: "The goal [of chemical biology] is a seamless application of chemical principles to decipher complexities in biology and bring scientists trained in chemistry to full engagement on biological projects," (2).


This is how I like to simplify the difference:

Adapted from (3). 

Biological Chemistry (aka Biochemistry): The study of the chemical properties of biological systems.
Traditionally, biochemists study biological systems in living organisms. They are interested in the role and function of biological molecules. Common techniques may include enzyme kinetics, mutagenesis, or pharmacology.

Chemical Biology: Manipulating biological systems using the tools/techniques of chemistry.
Conversely, chemical biologists might better be described as engineers. They want to use the tools of chemistry to study or "tweak" biological systems. Common techniques include directed evolution, metabolic engineering, or rational drug design.


Although I've just spent time developing a distinction between the two fields, many labs and many scientists frequently employ techniques of both in their research. For example, labs that are very skilled at synthesizing organic small molecules might also employ mutagenesis to tweak their enzyme target of interest (4). Or, a graduate student trained in biophysical methodology might elect to do a more chemically-oriented post-doc, applying fresh perspective to new problems.

Working at the intersection of biology and chemistry sometimes has interesting consequences, but I feel that one of the main barriers between these fields is the lack of cross-talk. Advances in one field may be overlooked, simply because the results are presented in an unfamiliar language. In my opinion, this is why interdisciplinary training is so valuable. Training in biochemistry or chemical biology allows scientists not only to "speak the language" of each field, but to apply the best techniques to the most interesting biological questions.




Additional Reading:
1. Thomas, P. "The Chemical Biologists," Harvard Magazine, 2005, 38-47.

References:
1. Mahapatra, A. "Chemistry or Biology? The debate continues..." ACS Chem. Biol. 2009, 4, 969-970.
2. Walsh, CT. "Natural Insights for Chemical Biologists,"Nat. Chem. Biol. 2005, 1, 122-144.
3. Calderone, CT. BIOL/CHEM 359. Lecture on Chemical Biology. Presented at Macalester College, St. Paul, MN, Sept. 8, 2010.
4. Shah, K. et al. "Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates," Proc. Natl. Acad. Sci. USA, 1997,  94, 3565-3570.

Hello and Welcome!

Welcome to Commitment to Catalysis (C2C)! Whether you were searching for this blog or came here via another website, I'm glad you took the time to visit.

This blog was created as a way for me to keep up to date with current chemical biology and enzymology research, as well as a way for me to work on scholarly writing. My goal is not only to make science understandable and accessible, but also fun! I strive to give an accurate analysis of updates in my field, but sometimes (due to lack knowledge or time…I mean, c’mon, I’m a grad student after all!) I miss something important. Please feel free to contact me with resources if you notice a gross error and I will do my best to make C2C an informed blog.

Who am I, you ask? I am currently a graduate student in the Chemistry and Chemical Biology Program at the University of California--San Francisco. My academic interests are in chemical biology, with a specific interest in enzymology and epigenetic modifications. I am also interested in promoting women in the sciences, as well as improving scientific education at all levels. When I'm not in lab I enjoy hiking and playing card games.

So stay tuned! Some new posts will be going up next week and I will attempt to update this blog about twice a week thereafter.