Introducing Our Authors pubs.acs.org/acschemicalbiology
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STIJN J. A. APER
Education: Boğaziçi University, Istanbul, Turkey - B.S. in Chemical Engineering, 2010; Yale University, New Haven, CT - M.S. in Biomedical Engineering, 2011, Advisor: Tarek Fahmy Current Position: Ph.D. Candidate at Columbia University in the Department of Chemical Engineering, Advisor: Scott Banta Nonscientific Interests: Traveling, playing the piano, a fan of Broadway Shows and NY Philharmonic My Ph.D. work focuses on rational protein design and modification. Using protein-engineering tools, I have been studying protein−protein interactions for various biotechnology applications, including stimulus responsive hydrogel formation and directed evolution of peptides for controllable biomolecular recognition. In this work, we have studied the interactions between mitochondrial malate dehydrogenase, citrate synthase, and aconitase of the TCA cycle. Understanding the metabolon formation and substrate channeling phenomena within these enzymes is important since the high efficiency of the TCA cycle, which is one of the most important processes for the cellular metabolism, crucially depends on them. Using both natural enzymes and their recombinant counterparts, we identified the amino acids responsible for the channeling among malate dehydrogenase and citrate synthase, which we further studied via mutational analysis. (Read Bulutoglu’s article DOI: 10.1021/acschembio.6b00523.)
Image courtesy of Leola Metzemaekers.
Education: B.S. and M.S. in Biomedical Engineering, TU/e, Advisor: Prof. Dr. Maarten Merkx Current Position: Ph.D. Candidate, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands; Advisor: Prof. Dr. Maarten Merkx Nonscientific Interests: Race cycling, tennis, playing trumpet in brass band, and reading My research focuses on the engineering of protein sensors and switches for intracellular imaging or the rewiring of cell signaling, using modular design strategies. This paper represents an example of such an approach, transforming two previously developed FRET sensors for Zn2+ imaging into BRET/FRET sensors by fusing the bright luciferase NanoLuc to the donor fluorescent protein. Without any additional optimization, the resulting sensors retained their FRET response and allowed BRET-based Zn2+ imaging in mammalian cells, both in suspension and in single cells. Using BRET for readout is mainly attractive for in vivo imaging, imaging in optogenetic measurements, and other applications in which external excitation is undesirable. Looking forward, I am particularly interested in applying either DNA- or protein-based engineering strategies for developing diagnostics or therapeutics. (Read Aper’s article DOI: 10.1021/acschembio.6b00453.)
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ROSS CHELOHA
BEYZA BULUTOGLU Image courtesy of Ron Lutz II.
Education: B.S. Chemistry, University of NebraskaLincoln, with Prof. David Berkowitz; Ph.D. Chemistry, University of WisconsinMadison, with Prof. Samuel Gellman Current Position: Postdoctoral researcher at the Whitehead Institute for Biomedical Research at Massachusetts Institute of Technology in the laboratory of Hidde Ploegh Nonscientific Interests: Hiking, camping, college football, and spending time with friends and family I am interested in synthesizing and using polypeptides that contain non-natural structural modifications to probe biological Published: October 21, 2016
Image courtesy of Mehmet Z. Baykara.
© 2016 American Chemical Society
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DOI: 10.1021/acschembio.6b00857 ACS Chem. Biol. 2016, 11, 2657−2660
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Introducing Our Authors
systems in ways not easily achieved using conventional peptides. My graduate research centered on studying the biological consequences of introducing structural modifications in the backbone of polypeptides. In this manuscript, we present a backbone-modified analogue of the parathyroid hormone (PTH) that effectively binds to the cognate receptor, blocks receptor activation, and dampens high levels of signaling at mutant receptors, all while exhibiting substantially improved proteolytic stability relative to the prototype. We used this analogue as a tool to understand how the susceptibility of peptides to proteolytic degradation affects the efficacy of PTH-receptor antagonists in mice. These findings will guide future efforts to design agents for treating diseases of PTH-receptor hyper-activation. My future research efforts will focus on dissecting polypeptide-mediated cellular signaling processes using tools provided by synthesis. (Read Cheloha’s article DOI: 10.1021/acschembio.6b00404.)
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phenolic derivatives. (Read Dhammaraj’s article DOI: 10.1021/ acschembio.6b00402.)
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TAWEESAK DHAMMARAJ
KRISTEN E. GARCIA
Image courtesy of Kristen E. Garcia.
Education: University of New Mexico, B.S. in Chemical Engineering, 2012 Current Position: Columbia University, Ph.D. Candidate in Chemical Engineering, Research Advisor: Scott Banta Nonscientific Interests: Homebrewing, blues dancing, cooking, and board games My graduate research is focused on engineering multienzyme complexes. In these complexes of sequential enzymes, intermediates can be channeled directly from one active site to the next without being released into the bulk solution. This substrate channeling can lead to increased reaction rates and overcoming unfavorable thermodynamics in the bulk environment. In the present article, we examined a complex of recombinant mitochondrial malate dehydrogenase and citrate synthase and compared the recombinant complex structure and kinetics to a natural metabolon, identifying key amino acids for channeling of the intermediate. We were able to use sitedirected mutagenesis to inhibit complex formation and substrate channeling. (Read Garcia’s article DOI: 10.1021/acschembio.6b00523.)
Image courtesy of Dr. Ruchilak Rattarom.
Education: Chiang Mai University, Chiang Mai, Thailand, B.Pharm.; Chulalongkorn University, Bangkok, Thailand, M.Sc. in Pharm. (Pharmaceutical Chemistry); Mahidol University, Bangkok, Thailand, Ph.D. in Biochemistry Current Position: Lecturer in Pharmaceutical Chemistry at Mahasarakham University, Mahasarakham, Thailand Nonscientific Interests: Cooking, music, movies, and books My Ph.D. research investigated the reactions of p-hydroxyphenylacetate 3-hydroxylase (HPAH) with various phenolic compounds. We found that HPAH can use various types of phenolic and aniline compounds as substrates. The catalytic activity of the enzyme was improved through rational engineering to obtain variants that are more effective than the wild-type enzyme. In this paper, the S146, which is more efficient than the wild-type enzyme in hydroxylation of 4-aminophenylacetate, was obtained. Multiple turnover reactions of HPAH coupled with a NADH regenerating system can be used to convert the substrate into single- and doublehydroxylated products. The hydroxylation of 4-aminophenylacetate is more efficient at lower pHs. Presteady kinetics was used to investigate the pH effect on the HPAH reaction. Findings in this work imply that HPAH can be used as a biocatalyst to synthesize hydroxylated aniline compounds. A similar rational engineering principle may be used to generate variants of other enzymes homologous to HPAH that are capable of hydroxylating aniline compounds in addition to
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INMACULADA IZQUIERDO-BUENO
Image courtesy of Javier Moraga Galindo.
Education: University of Cádiz, Spain, B.S. in Environmental Science and B.S. in Marine Science, 2012; University of Cádiz, M.S. in Chemical Science and Technology, specialist in biomolecules, 2013 2658
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Current Position: Predoctoral fellow at University of Cádiz, Spain, in the “Chemical Biology: Biosynthetic Design of Fungicides” research group with Prof. Isidro G. Collado Nonscientific Interests: Shopping, cooking, and music My current research focuses on the study and discovery of novel natural products from fungi and their isolation, characterization, and biological evaluation toward the development of bioactive molecules. Advances in genomic studies, along with DNA sequencing, have given us a lot of information about the biosynthesis of natural products as well as the mechanisms through clusters of genes that can be modified to produce a new range of compounds. We know that the number of genes encoding biosynthetic enzymes in Botrytis cinerea clearly outnumbers the known secondary metabolites of these organisms. The deletion of the botrydial gene cluster has led to isolation of new cryptic metabolites from B. cinerea, proving to be a promising strategy for the isolation of new bioactive molecules. (Read Izquierdo-Bueno’s article DOI: 10.1021/acschembio.6b00581.)
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Introducing Our Authors
FEI WU
Image courtesy of Wenjie Ma.
Education: Nankai University, B.S. in Pharmacy, 2009; University of Utah, Ph.D. in Chemistry, 2015 Current Position: Chinese Academy of Science, Institute of Chemistry, Postdoc fellow at the Key Laboratory of Analytical Chemistry for Living Biosystems Nonscientific Interests: Reading, traveling, photography, swimming, and playing badminton My Ph.D. thesis was centered on the tricarboxylic acid (TCA) cycle metabolon, which is a highly efficient supramolecular catalytic complex composed of the eight TCA cycle enzymes. To elucidate such a sophisticated multienzyme association, my research involved microfluidic techniques and unraveled the intermediate-driven mechanism for metabolon formation. Using cross-linking mass spectrometry and computer simulation, I also resolved the structure of a mitochondrial malate dehydrogenase (mMDH)−citrate synthase (CS)−aconitase (ACO) octamer in vivo and identified key residues for protein−protein interactions. In our study presented in ACS Chemical Biology, a recombinant mMDH−CS complex was constructed according to its wild-type counterpart. By structural and kinetic probing through MS-docking and transient-time analysis, we proved that our engineered enzyme complex is a close mimic of the natural metabolon. (Read Wu’s article DOI: 10.1021/acschembio.6b00523.)
YAN QIN
Image courtesy of Zhongbin Qin.
Education: Nanjing University, B.S. Biology, 2000; Nanjing University, M.S. Physiology, 2003; Ohio University, Ph.D. in Neuroscience 2008, Advisor: Robert A Colvin; University of Colorado at Boulder, postdoctoral research associate with Amy E. Palmer, 2009−2015 Current Position: Assistant Professor, Department of Biological Sciences, University of Denver Nonscientific Interests: Swimming, hiking, and reading My lab is focused on developing fluorescent sensors for zinc ions and exploring zinc dynamics in living cells. Zinc is an essential biological ion, and it can function as cellular signals within and between cells. Due to its low concentrations, zinc in a dynamic cellular environment can only be detected by sensitive optical probes. We created a new type of zinc biosensors based on single fluorescent protein. Compared to previously published FRET sensors, these new sensors are simpler to image, require less sophisticated microscopes, and have decreased spectral bandwidth, allowing for multiple sensors to be used simultaneously. Our future work aims to expand the toolbox of single fluorescent protein based zinc sensors with new spectral and dynamic traits. (Read Qin’s article DOI: 10.1021/acschembio.6b00442.)
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QINGFEI ZHENG
Image courtesy of Ling Zhang.
Education: Tsinghua University, B.S. in Chemical Biology, 2012 Current Position: Ph.D. student at State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute 2659
DOI: 10.1021/acschembio.6b00857 ACS Chem. Biol. 2016, 11, 2657−2660
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Introducing Our Authors
of Organic Chemistry, Chinese Academy of Sciences, Advisor: Prof. Wen Liu Nonscientific Interests: Reading, snorkeling, swimming, basketball, table tennis, skating, and traveling My thesis work mainly focuses on the enzymology involved in the biosynthesis of structurally complex natural products and their metabolic pathway engineering. What interests me most is the development of new chemical tools for investigating elusive biological processes and to produce novel chemical architectures using engineered biological systems. In the previous work, we developed a strategy named precursor-directed mutational biosynthesis to generate derivatives of thiostrepton, a typical member of ribosomally synthesized and post-translationally modified peptides. Using this strategy, we obtained several thiostrepton derivatives and discovered a novel dual mode of action of thiostrepton against intracellular pathogens by utilizing these derivatives as chemical probes. In this work, we intended to produce more thiostrepton derivatives through the same method, but unexpectedly a new shut product without outstanding biological activities was obtained. This unusual result promoted us to pay more attention to the genes probably responsible for the oxidative modifications on the thiostrepton skeleton. Combining gene inactivation, exogenous chemical feeding, and in vitro assays, we assigned the functions of two cytochromes P450 in thiostrepton biosynthesis. This work shows that precursor-directed mutational biosynthesis can not only be used to expend molecular diversities but also be used to probe complex biosynthetic logics. (Read Zheng’s article DOI: 10.1021/acschembio.6b00419.)
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DOI: 10.1021/acschembio.6b00857 ACS Chem. Biol. 2016, 11, 2657−2660
