NMR Spectroscopy Topical Group Meetings

The North Jersey ACS NMR Topical Group proudly presents its June meeting of 2013 at Rutgers CABM on Wednesday, June 12, 2013.  [ register ]

This meeting is sponsored by

Featured Speakers

Talk I
19F NMR as a Direct Probe of Intermolecular Interactions by Non-Structural Protein 1 from Influenza A Virus

James M. Aramini, PhD,

Research Assistant Professor, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ

Talk II
“Nexomics Biosciences”

Gregory Kornhaber, PhD,
Nexomics Biosciences, North Brunswick, NJ

Abstract for Talk I:

Non-structural protein 1 of influenza A virus, NS1A, is a key multifunctional virulence factor produced in the infected host cell that plays a critical role in evading the host antiviral response. This highly conserved hub protein in influenza infection is comprised of two domains: an N-terminal double-stranded RNA-binding domain (RBD) and a C-terminal effector domain (ED) which binds to a plethora of host cellular proteins. Isolated RBD and ED domains of NS1A both exist as homodimers in solution.

Since the 1960s, 19F has been recognized as a valuable NMR probe for biological systems due to its numerous favorable NMR properties, including its nuclear spin (I = ½), high natural abundance (100%), extremely high sensitivity, wide chemical shift range, minimal inherent background 19F signals, and the exquisite sensitivity of its chemical shift to changes in local environment.

Here we have applied 19F NMR to the study of NS1A from influenza A/Udorn/307/1972 (H3N2) virus. We incorporated 5-fluorotryptophan (5-F-Trp) into NS1A RBD, NS1A ED, and full-length NS1A, and assigned the 19F signals corresponding to the four Trp residues in this protein by site directed mutagenesis. We demonstrate that the 19F signal for W187, located in a functionally important helix-helix interface, can be used to monitor the oligomerization state of the ED (i.e., dimer to monomer transitions). Our 19F NMR data provide strong evidence in favor of conformational exchange at this critical interface in solution. Moreover, for full-length NS1A, 19F NMR provides the first direct spectroscopic evidence that W187, which is known to mediate intermolecular ED:ED interactions in the oligomerization of full-length NS1A, becomes solvent-exposed at protein concentrations below aggregation (ca. 50 %mu;M). Finally, we demonstrate that 5-F-Trp and 4-fluorophenylalanine (4-F-Phe) incorporation combined with 19F NMR serves as a sensitive approach for monitoring the binding of the F2F3 peptide from CPSF30 to NS1A ED.

This work was supported by grants from the NIGMS Protein Structure Initiative U54-GM094597 (to G.T.M.), NIH U01-AI074497 (to G.T.M. and R.M.K.), and NIH R01-AI11772 (to R.M.K.).

The North Jersey ACS NMR Topical Group proudly presents its May meeting of 2013 at the Fuji Japanese Sushi & Seafood  Rutgers CABM on Wednesday, May 15, 2013.  [ register ]

Abstract for Talk I:

Biological macromolecules are inherently dynamic and in many cases depend on changes in conformation and flexibility to perform their physiological roles. In order to understand how they function at an atomic level, it is necessary to map the energetic interactions that govern their structures and dynamics. NMR spectroscopy is well suited to addressing this problem, since it can provide detailed information on molecular conformation and internal motions. Many NMR measurements can be interpreted quantitatively in terms of exchange rates or thermodynamic differences between conformational states, such as folded and unfolded or ligand-free and ligand-bound forms. In this regard, biological NMR data are highly complementary to those of biocalorimetry, for example isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC). These methods directly detect the heat absorbed and released during protein binding and folding reactions. In fact, the combination of calorimetric and NMR methods provides a clearer picture of molecular processes than does either technique alone. Microcalorimetry is extremely sensitive to the energetics of conformational transitions and macromolecular interactions. However it can be difficult to relate these measurements to specific changes in molecular structure and flexibility without additional information. Conversely, NMR is sensitive to conformation and dynamics at the level of individual atoms, but thermodynamic information is obtained indirectly. Combining NMR and calorimetric measurements has the potential to improve our understanding of how macromolecular structure, dynamics, energetics and function are related, and to redefine our description of biological systems at the atomic level. I will discuss some recent examples from our lab in which NMR and calorimetry have been applied in concert to study fundamental aspects of protein function including folding, molecular recognition, and allostery. 

The North Jersey ACS NMR Topical Group proudly presents its March meeting at the Fuji Japanese Sushi & Seafood on Wednesday, March 20, 2013.  [ register ]

This meeting is sponsored by Advanced Chemistry Development, Inc. (ACD/Labs)

Featured Speakers

Talk I
“ACD/Lab’s Spectrus NMR Workbook: A Toolkit for Pharma’s NMR Spectroscopist”

Dr. Janet Caceres-Cortes
Principal Scientist, DAS NMR, Bristol-Myers Squibb
Route 206 & Provinceline Road
Princeton, NJ 08543-4000

Talk II
“Current Developments at ACD/Labs in Tools to Assist the NMR Spectroscopist”

Patrick Wheeler
Product Manager – NMR, Advanced Chemistry Development, Inc.
8 King Street East, Suite 107
Toronto, ON Canada M5C 1B5

Abstract for Talk I:

The potential role of metabolites in drug efficacy and safety underscores the importance of detecting and characterizing drug metabolites notwithstanding the often complex metabolic profiles and generation of numerous metabolites of varying concentrations from the drugs of interest. Thus, metabolite identification (ID) studies are an integral part of pre-clinical and clinical drug development activities and in many instances rely on Nuclear Magnetic Resonance (NMR) spectroscopy.

ACD/NMR Workbook provides an array of tools allowing processing of 1D and 2D data. It allows the NMR spectroscopist to perform structure elucidation and identify metabolite modification sites while recording their spectral assignments. A useful practice in metabolite ID is to compare the structural information attained through the analysis of chemical shifts, coupling constants, peak integrations and correlations for the isolated metabolite with those of the parent compound. This is not always a facile endeavor since the quality of the metabolite NMR spectra can be challenged by sensitivity, dynamic range, and matrix interferences. ACD/NMR Workbook has a number of features that facilitate this comparison. This presentation will highlight the new and enhanced features of Spectrus/NMR Workbook over ACD12/Workbook and its utility for metabolite ID and structure elucidation.

The North Jersey ACS NMR Topical Group proudly presents its February meeting at the Fuji Japanese Sushi & Seafood on Wednesday, February 20, 2013.

Abstract:

Multidrug resistance (MDR) is a pervasive clinical problem that reduces the effectiveness of treatment against bacterial infections, viral infections, and cancer. Efflux of drugs across the lipid bilayer by MDR membrane protein transporters is one way in which resistance is conferred to the host organism or cell. To derive a structure/function relationship for this class of proteins, our study uses the small multidrug resistance (SMR) family as a model system for deciphering the mechanism of transport with the long-term goal of decoding the evolutionary importance of the transporter family. We used solid-state NMR (SSNMR) spectroscopy to study the topology and structure of EmrE in liposomes (magic-angle-spinning or MAS) and magnetically aligned lipid bilayers (oriented SSNMR or O-SSNMR). The MAS experiments were used to map chemical shift perturbations upon drug binding while the O-SSNMR experiments revealed the change in helix orientation upon binding and transport. Together these complementary techniques showed that drug binding perturbs both the structure of EmrE as well as the helical orientations with respect to the lipid bilayer.

The North Jersey ACS NMR Topical Group proudly presented its January meeting at the Fuji Japanese Sushi & Seafood on Wednesday, January 16, 2013.

The North Jersey ACS NMR Topical Group proudly presented its November meeting at the Fuji Japanese Sushi & Seafood on Wednesday, November 14, 2012.

Abstract

The 2D structure of most small molecules can be in principle straightforwardly determined by manual or automatic analysis of a set of experimental data that includes the molecular formula, a series of 1D and 2D NMR experiments providing through-bond connectivity (COSY, TOCSY, HSQC, HMBC and ADEQUATE/INADEQUATE based experiments), and chemical shift predictions.

This is the main concept embedded in automatic structure elucidation programs. Once the 2D structure is available, the determination of the relative spatial arrangement (configuration and preferred conformation) of all atoms in the molecule is a more challenging task that it is commonly addressed in NMR by using NOE and 3J coupling constants analysis, as well as recent developments on the application of DFT calculation of 13C chemical shifts.

However, it is difficult to assess how many samples are sitting on the laboratory’s refrigerators waiting for an independent methodology that could lift some of the ambiguities generated by the use of conventional NMR methods. The development of the application of Residual Dipolar Couplings (RDCs) to the configurational and conformational analysis of small molecules has matured enough in the recent years to perform this task in an almost straightforward way, without even the need of using NOE and 3J coupling analysis, as it will be presented here for the analysis of rigid and semi-rigid small molecules.

The application of RDCs to the analysis of flexible molecules is still a field of research with plenty of room for development and a generally accepted approach is not available yet.