Associate Professor of Biochemistry and Physical Biochemistry

Publications | Research | Faculty

Background:

Linda Nicholson is an Associate Professor of Molecular Biology and Genetics. She received B.Sc. and M. Sc. degrees in Mechanical Engineering from the University of Virginia in 1982 and 1985, respectively. In 1990, she received a Ph.D. in Molecular Biophysics from Florida State University, where she specialized in solid-state NMR studies to uniformly oriented biomolecular systems. As a postdoc at NIH, she worked in the rapidly developing field of multidimensional solution NMR spectroscopy of proteins. She joined the Cornell faculty in 1994.

Courses Taught:

BioBM 631 - Protein Structure, Function & Dynamics

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Research Focus:

Professor Nicholson's research is funded by a grant from the National Science Foundation, "Protein Phosphorylation as a Biophysical Switch: NMR Determination of Structural and Dynamic Responses to Phosphorylation", by a Shannon Award from the National Cancer Institute, and by the New York State Hatch Program.

Life takes place through the concerted flow of numerous biological processes. At the molecular level, this involves highly specific and transient protein-protein and protein-ligand interactions. The specificity and function of a given protein is determined by its unique three-dimensional structure and by motions of groups of atoms within this scaffold. We are interested in observing changes in atomic level structure and dynamics induced by perturbations, such as ligand binding or phosphorylation, that are associated with these transient interactions. Such information provides insights into unanswered questions regarding the origins of binding energy and the mechanisms by which protein function is regulated. These questions are critical in practical endeavors such as drug design and protein engineering.

Our research involves the application of multidimensional NMR spectroscopy to investigate the structure and dynamics of proteins in different functional states. We are focusing on key proteins that have been shown to play important roles in biological processes such as thiamin biosynthesis, intracellular trafficking, viral replication, and signal transduction. Many of these proteins are implicated in disease processes such as Alzheimer’s disease, diabetes, AIDS, and cancer. A few of these systems are described briefly below.

We have recently determined the structure of ThiS, a sulfur carrier protein in the E. coli thiamin biosynthesis pathway. Although ThiS shares little sequence identity with ubiquitin, the two proteins share a remarkable structural resemblance. Combined with striking functional similarities, this result indicates that the eukaryotic ubiquitin and the prokaryotic ThiS evolved from a common ancestor. This provides an elegant example of how nature has utilized a basic structure-mechanism unit as a building block in widely different biological processes. This collaboration with Tadhg Begley and his lab provides future opportunities for studies of ThiS in complex with other thiamin biosynthesis pathway proteins, which will not only shed light on the mechanism of sulfur transfer in biosynthesis but will also enhance our understanding of the initial steps of the ubiquitin conjugation pathway.

The 47-residue cytoplasmic C-terminal domain of the amyloid precursor protein (APP) plays important roles in endocytosis of APP and possibly in signal transduction. We are interested in the putative signal sequences for internalization and targeting to the lysosomes, since lysosomal processing of APP is thought to be a key pathway in generating amyloidogenic fragments. How are these target sequences recognized by other proteins, resulting in the internalization and processing of APP? How might these interactions be blocked, preventing lysosomal generation of amyloidogenic fragments of APP? Through NMR studies of this cytoplasmic tail and its various phosphorylated forms we hope to shed light on the mechanisms of interaction between APP and cellular factors, elucidating potential targets for the rational design of drugs to inhibit the progression of Alzheimer’s disease.

Retroviral proteases (PRs), which are essential for viral replication, must dimerize to become active. In collaboration with Volker Vogt and his lab, we are pursuing structural studies of an inactive, monomeric mutant form of the Rous sarcoma virus PR which is missing the first three N-terminal amino acids. This structure may provide clues to the nature of protease dimerization and its control, and will provide valuable insights for drug design strategies to block dimerization, which could be extended to other retroviruses such as HIV.

The proto-oncoprotein pp60^c-src (Src) is an important signal transduction protein that has been implicated in several carcinomas, including breast and colon cancer. How is Src is activated by specific phosphorylation events? What role do internal protein motions play in determining the strength of ligand binding to the SH3 domain? We are addressing these and other questions to aid in our understanding of the biophysical basis for carcinogenesis.

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Papers:

Click here to view Dr. Nicholson's PubMed listings.

T. Yamazaki, L.K. Nicholson, D.A. Torchia, S.J. Stahl, P.T. Kaufman, P.T. Wingfield, P.J. Domaille, and S. Campbell-Burk (1994). "Secondary Structure and Signal Assignments of HIV-1 Protease Complexed to a Novel, Structure Based Inhibitor" Eur. J. Biochem. 219, 707-712.

S. Grzesiek, A. Bax, L.K. Nicholson, T. Yamazaki, P.T. Wingfield, S.J. Stahl, C.J. Eyermann, D.A. Torchia, C.N. Hodge, P.Y.S. Lam, P.K. Jadhav, and C.-H. Chang (1994). "NMR Evidence for the Displacement of a Conserved Interior Water Molecule by a Non-peptide Cyclic Urea Based HIV Protease Inhibitor", J. Am. Chem. Soc. 116, 1581-1582.

J.-H. Yeo, M. Demura, T. Asakura, T. Fujito, M. Imanari, L.K. Nicholson, and T.A. Cross (1994). "A Structural Analysis of Highly Oriented Poly(p=phenylene-terephthalamide) by Solid State NMR", Solid State NMR 3, 209-218.

T. Yamazaki, L.K. Nicholson, P.T. Wingfield, S.J. Stahl, P.T. Kaufman, P.J. Domaille, and D.A. Torchia (1994). "NMR and X-Ray Evidence that the HIV Protease Catalytic Aspartyl Groups Have an Essential Role in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor", J. Am. Chem. Soc. 116, 10791-10792.

L.K. Nicholson, S. Grzesiek, T. Yamazaki, S.J. Stahl, P.T. Kaufman, P.T. Wingfield, P.J. Domaille, A. Bax, and D.A. Torchia (1995). "Flexibility and Function in the HIV-1 Protease", Nature Struct. Biol. 2, 274-280.

L.K. Nicholson, C.-H. Chang, and C.N. Hodge (1996). "Flexibility and Function in the HIV-1 Protease", in NMR in Drug Design (D. Craik, Ed.), CRC Press, Inc.

L.K. Nicholson, L.E. Kay, and D.A. Torchia (1996). "Protein Dynamics as Studied by Solution NMR Techniques" In NMR Spectroscopy and its Application to Biological Research, (S. Sarkar, Ed.), Elsevier Science Publishers.

T. Yamazaki, A.P. Hinck, Y.-X. Wang, L.K. Nicholson, D.A. Torchia, P. Wingfield, S.J. Stahl, D. Kaufman, C.-H. Chang, P.J. Domaille and P.Y.S. Lam (1996). Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy. Protein Science 5, 495-506.

M. Tessari, L.N. Gentile, S.J. Taylor, D.I. Shalloway, L.K. Nicholson, and G.W. Vuister (1997). "Heteronuclear NMR Studies of the Combined SH3-SH2 Domains of pp60^c-Src:the Effects of Phosphopeptide Binding." Biochemistry 36: 14561-14571.

A.P. Loh, W. Guo, et al. (1999). "Backbone dynamics of inactive, active, and effector-bound Cdc42Hs from measurements of (15)N relaxation parameters at multiple field strengths." Biochemistry 38(39): 12547-57.

T.A. Ramelot, L.N. Gentile, et al. (2000). "Transient structure of the amyloid precursor protein cytoplasmic tail indicates preordering of structure for binding to cytosolic factors." Biochemistry 39(10): 2714-25.

G. Zhu, Y. Xia, et al. (2000). "Protein dynamics measurements by TROSY-based NMR experiments." J Magn Reson 143(2): 423-6.

F. Cordier, C. Wang, S. Grzesiek, and L.K. Nicholson. (2000). Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR. J. Mol. Biol. 304:497-505.

Wang, C., Xi, J., Begley, T. P. and Nicholson, L. K. (2001) Solution Structure of ThiS and Implications for the Evolutionary Roots of Ubiquitin, Nature Structural Biology, 8, 47-51.

Loh, A. P., Pawley, N. H., Nicholson, L. K. and Oswald, R. E. (2001) An increase in side chain entropy facilitates effector binding: NMR characterization of the side chain methyl group dynamics in cdc42Hs, Biochemistry 40(15), 4590-4600.

Reinking, J. L., Schatz, G. W., Vogt, V. and Nicholson, L. K. (2001) Letter to the Editor: 1H, 15N and 13C chemical shift assignments of a monomeric N-terminal deletion mutant of the Rous sarcoma virus protease, J. Biomol. NMR 19, 279-280.

Schatz, G. W., Reinking, J., Zippin, J., Nicholson, L. K. & Vogt, V. M. (2001). Importance of the N terminus of rous sarcoma virus protease for structure and enzymatic function. J Virol 75(10), 4761-70.

Pawley, N. H., Wang, C., Koide, S. and Nicholson, L. K. (2001) An Improved Method for Distinguishing Between Anisotropic Tumbling and Chemical Exchange in Analysis of 15N Relaxation Parameters, J. Biomol. NMR 20, 149 - 165.

Wang, C., Pawley, N. H. & Nicholson, L. K. (2001) The Role of Backbone Motions in Ligand Binding to the c-Src SH3 Domain. J. Mol. Biol. 313, 873-887.

Wulf, J., Pascuzzi, P., Martin, G. and Nicholson, L. K. (2002) "Letter to the Editor: 1H, 15N and 13C chemical shift assignments of the structured core of the Pseudomonas effector protein AvrPto", J. Biomol. NMR 23, 247-248.

Pawley, N. H., Koide, S. and Nicholson, L. K. (2002) "Backbone Dynamics and Thermodynamics of Borrelia Outer Surface Protein A", J. Mol. Biol, in press.

Pawley, N. H., Gans, J. D. and Nicholson, L. K. (2002) "Factors Determining the Reliable Description of Global Tumbling Parameters in Solution NMR", J. Biomol. NMR, in press.

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