Department of Chemistry

Biochemistry & Chemical Biology

Research ImageGraduate students in biochemistry and chemical biology meld molecular and structural biology with physical, organic and analytical chemistry to understand the molecular basis of biological processes and of human disease. Research in the Biochemistry and Chemical Biology Division focuses on the structure and function of proteins, membranes, DNA, RNA, large macromolecular complexes and viruses, natural product biogenesis, synthetic biology, and genomics.

Students are a constant source of new hypotheses for mechanisms underlying cellular machines like the ribosome and spliceosome, and for the protein and RNA folding problems. Students tackle these problems using biochemical methods, chemical biosensor technologies, protein and nucleic acid crystallography, in vitro and in vivo evolution, multi-dimensional NMR spectroscopy, surface chemistry, atomic force microscopy, fluorescence spectroscopy, and high-resolution mass spectrometry.

Doctoral students in Biochemistry and Chemical Biology leave the Department broadly trained for leadership roles in academia and industry.

 

 

 

SHAPE-MaP RNA Structure Analysis

Many central biological processes are mediated by complex RNA structures, but the higher-order interactions for most RNAs are unknown, which makes it difficult to understand how RNA structure governs function. As published in Nature Methods, a team of students in the Weeks lab have invented a new approach -- selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) -- that makes possible de novo and large-scale identification of RNA functional motifs.

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SHAPE-MaP melds chemistry invented in the Weeks lab with readout by massively parallel sequencing to make it possible to detect structure-selective chemical reactions in RNA on genome-wide scales. SHAPE-MaP represents a "no compromises" approach for interrogating the structure of RNA, enables analysis of low-abundance RNAs, and is ultimately poised to democratize RNA-structure analysis.

 

Protein Stability in Living Cells

The intracellular milieu differs from the dilute conditions in which most biophysical and biochemical studies are performed. This difference has led both experimentalists and theoreticians to tackle the challenging task of understanding how the intracellular environment affects the properties of biopolymers. Despite a growing number of in-cell studies, there is a lack of quantitative, residue-level information about equilibrium thermodynamic protein stability under nonperturbing conditions.

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William Monteith and Professor Gary Pielak, published in PNAS, report the use of NMR-detected hydrogen–deuterium exchange of quenched cell lysates to measure individual opening free energies of the 56-aa B1 domain of protein G (GB1) in living Escherichia coli cells without adding destabilizing cosolutes or heat. Comparisons to dilute solution data, pH 7.6 and 37 °C, show that opening free energies increase by as much as 1.14 ± 0.05 kcal/mol in cells. Importantly, this research also shows that homogeneous protein crowders destabilize GB1, highlighting the challenge of recreating the cellular interior. William and Gary discuss their findings in terms of hard-core excluded volume effects, charge–charge GB1-crowder interactions, and other factors. The quenched lysate method identifies the residues most important for folding GB1 in cells, and should prove useful for quantifying the stability of other globular proteins in cells to gain a more complete understanding of the effects of the intracellular environment on protein chemistry.

 

Representative Publications

Cell-Mediated Assembly of Phototherapeutics. Weston J. Smith, Nathan P. Oien, Robert M. Hughes, Christina M. Marvin, Zachary L. Rodgers, Junghyun Lee and David S. Lawrence. Angewandte Chemie International Edition, Volume 53, Issue 41, pages 10945-10948, October 6, 2014.

Optogenetic Engineering: Light-Directed Cell Motility. Robert M. Hughes and David S. Lawrence. Angewandte Chemie International Edition, Volume 53, Issue 41, pages 10904-10907, October 6, 2014.

RNA Motif Discovery by SHAPE and Mutational Profiling (SHAPE-MaP). Nathan A Siegfried, Steven Busan, Greggory M Rice, Julie A E Nelson & Kevin M Weeks. Nature Methods 11, 959–965 (2014).

Residue Level Quantification of Protein Stability in Living Cells. William B. Monteith and Gary J. Pielak. PNAS July 21, 2014, doi: 10.1073/pnas.1406845111 .

Nitric Oxide-Releasing Quaternary Ammonium-Modified Poly(amidoamine) Dendrimers as Dual Action Antibacterial Agents. Brittany V. Worley , Danielle L. Slomberg , and Mark H. Schoenfisch. Bioconjugate Chem., 2014, 25 (5), pp 918–927.

Protein Crowder Charge and Protein Stability. Mohona Sarkar, Joe Lu, and Gary Pielak. Biochemistry, 2014, 53 (10), pp 1601–1606.

Strategies for Protein NMR in Escherichia coli. Guohua Xu, Yansheng Ye, Xiaoli Liu, Shufen Cao, Qiong Wu, Kai Cheng, Maili Liu, Gary J. Pielak, and Conggang Li. Biochemistry, 2014, 53 (12), pp 1971–1981.

Long-Wavelength Fluorescent Reporters for Monitoring Protein Kinase Activity. Nathan P. Oien, Luong T. Nguyen, Dr. Finith E. Jernigan, Prof. Melanie A. Priestman and Prof. David S. Lawrence. Article first published online: 6 MAR 2014, DOI: 10.1002/anie.201309691.

Low Copy Numbers of DC-SIGN in Cell Membrane Microdomains: Implications for Structure and Function. Ping Liu, Xiang Wang, Michelle S. Itano, Aaron K. Neumann, Aravinda M. de Silva, Ken Jacobson, Nancy L. Thompson. Traffic, Volume 15, Issue 2, pages 179–196, February 2014.

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure. Jillian Tyrrell, Jennifer L. McGinnis, Kevin M. Weeks, and Gary J. Pielak . Biochemistry, Article ASAP, DOI: 10.1021/bi401207q.