Dr. Michael Latham
Principal Research Interests
- Solution State Biomolecular NMR
- Structural Biology
- Protein dynamics
- DNA Damage Repair
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for biomolecular structure determination and dynamics studies. This potential to site-specifically probe dynamics is highlighted by the ability to quantitatively assess the structure, kinetics and thermodynamics of sparsely populated conformations that are invisible to other biophysical techniques and are often important for catalysis, ligand binding and allostery. While traditional NMR approaches for structural and dynamics studies can routinely be applied to proteins with molecular masses < 25-35 kDa, advances in labeling (deuteration), methodology (Transverse Relaxation Optimized SpectroscopY - TROSY) and hardware (larger magnetic field and cryoprobes) have made quantitative studies of proteins approaching 100 kDa in molecular mass tractable. This range can be extended even further by leveraging the more favorable spectroscopic properties of 13CH3 – labeled methyl side-chains in an otherwise highly deuterated background. Methyl groups generally give better signal than the backbone amide groups, and since Ile, Leu, Val residues represent ~25% of protein side-chains and are distributed throughout protein structures in the hydrophobic core, binding interfaces and catalytic sites, they represent sensitive probes of macromolecular structure and dynamics. In fact, using these methyl TROSY techniques, macromolecular complexes with molecular masses approaching 1 MDa have been studied.
DNA Double Strand Break Repair
DNA double-stranded breaks (DSBs) are a particularly harmful form of DNA damage resulting from a variety of internal and external factors. Failure to protect against or correct DSBs leads to genomic instability and potentially to carcinogenesis. The central player in recognizing DSBs is the Mre11-Rad50-Nbs1 (MRN) complex. Mre11 and Rad50 are strictly conserved across all forms of life, while Nbs1 is found only in eukaryotes.
The nuclease Mre11 forms a homodimer via hydrophobic interactions that results in a U-shaped DNA binding site. Rad50 is an ABC ATPase protein; a central Zn hook and 500 Å long anti-parallel coiled-coil bring the N- and C-terminal domains into proximity forming the functional ABC ATPase. Upon binding of ATP, Rad50 also dimerizes. In the MRN complex, a Rad50 ABC ATPase domain interacts with each of the Mre11 subunits in the homodimer (M2R2) to form the sensing and processing core of the MRN complex. The ATPase activity of Rad50 regulates the conformation of M2R2: binding of ATP results in a closed M2R2 structure, which opens upon ATP hydrolysis. While both conformations can bind to DNA, only the open state is capable of Mre11 nuclease activity.
The present understanding of the structural underpinnings for the role of the MRN complex in DNA damage response is limited to several high resolution crystal structures of sub-domains, sometimes in the presence of ligand or peptide fragments of binding partners. The research performed in the lab aims to build upon this work and gain greater insight into the overall architecture of the MRN complex through the use of methyl TROSY solution NMR methodologies. Methyl groups are being used as probes for determining structures of M2R2 in complex with DNA in the presence and absence of ATP. These structural models will give the first indication for how the MRN complex senses a DSB and the precise role of the nucleotide bound states of Rad50. Furthermore, a better understanding will be obtained for the effect of disease-causing mutations, post-translational modifications and downstream effector binding on MRN function.
- Increasing the buffering capacity of minimal media leads to higher protein yield. Azatian SB, Kaur N, Latham MP. J Biomol NMR. 2019 73(1-2):11-17.
- Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes. Boswell ZK, Latham MP. Biochemistry. 2019 58(3):144-155. 26.
- The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity. Grozdanov PN, Masoumzadeh E, Latham MP, MacDonald CC. Nucleic Acids Res. 2018 46(22):12022-12039.
- A dynamic allosteric pathway underlies Rad50 ABC ATPase function in DNA repair. Boswell ZK, Rahman S, Canny MD, Latham MP. Sci Rep. 2018 8(1):1639
- Latham MP, Kay LE (2014) "A similar in vitro and in cell lysate folding intermediate for the FF domain." J Mol Biol. 426(19):3214-20.
- Sekhar A, Latham MP, Vallurupalli P, Kay LE (2014) "Viscosity-dependent kinetics of protein conformational exchange: microviscosity effects and the need for a small viscogen." J Phys Chem B. 118(17):4546-51.
- Latham MP, Sekhar A, Kay LE (2014) "Understanding the mechanism of proteasome 20S core particle gating." Proc Natl Acad Sci USA. 111(15): 5532-7.
- Xiao Y, Lee T, Latham MP, Warner LR, Tanimoto A, Pardi A, Ahn NG (2014) "Phosphorylation releases constraints to domain motion in ERK2." Proc Natl Acad Sci USA. 111(7): 256-11.
- Latham MP, Kay LE (2013) "Probing non-specific interactions of Ca²⁺ -calmodulin in E. coli lysate." J Biomol NMR. 55(3): 239-47.
- Latham MP, Kay LE (2012) "Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate." PLoS One. 7(10): e48226.
- Latham MP, Zimmermann GR, Pardi A (2009) "NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer." J Am Chem Soc. 131(14): 5052-3.
- Latham MP, Hanson P, Brown DJ, Pardi A (2008) "Comparison of alignment tensors generated for native tRNAval using magnetic fields and liquid crystalline media." J Biomol NMR. 40(2): 83-94.
- Latham MP, Brown DJ, McCallum SA, Pardi A (2005) "NMR methods for studying the structure and dynamics of RNA." Chembiochem. 6(9): 1492-505.