Training Program in Protein Folding

Publications by Trainees and Travel Awardees of the Program

2014

Bareti, D. and R. L. Williams (2014). "PIKKs — the solenoid nest where partners and kinases meet." Current Opinion in Structural Biology 29(0): 134-142.

Rizzolo, K., P. Wong, et al. (2014). The Interaction Network of the Hsp90 Molecular Chaperone. Interactomics & Systems Biology: The Molecular Chaperones Interaction Networks in Protein Folding and Degradation. W. A. Houry. New York, Springer Science + Business Media.

Sun, Y., P. E. Arslan, et al. (2014). "Binding of TDP-43 to the 3'UTR of its cognate mRNA enhances its solubility." Biochemistry 53(37): 5885-5894.

Vlasblom, J., K. Zuberi, et al. (2014). "Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli." Bioinformatics.

Weichert, A., A. S. Besemer, et al. (2014). "Wild-type Cu/Zn superoxide dismutase stabilizes mutant variants by heterodimerization." Neurobiology of Disease 62: 479-488.

2013

Christian, P., Sacco, J. & Adeli, K. Autophagy: Emerging roles in lipid homeostasis and metabolic control. Biochim Biophys Acta 1831, 819-824, (2013).

Hansen, A. L., Bouvignies, G. & Kay, L. E. Probing slowly exchanging protein systems via (1)(3)Calpha-CEST: monitoring folding of the Im7 protein. J Biomol NMR 55, 279-289, (2013).

Kim, T. H., Chung, K. Y., Manglik, A., Hansen, A. L., Dror, R. O., Mildorf, T. J., Shaw, D. E., Kobilka, B. K. & Prosser, R. S. The role of ligands on the equilibria between functional states of a G protein-coupled receptor. J Am Chem Soc 135, 9465-9474, (2013).

Kumar, A., Burns, D. C., Al-Abdul-Wahid, M. S. & Woolley, G. A. A circularly permuted photoactive yellow protein as a scaffold for photoswitch design. Biochemistry 52, 3320-3331, (2013).

Latham, M. P. & Kay, L. E. Probing non-specific interactions of Ca(2)(+)-calmodulin in E. coli lysate. J Biomol NMR 55, 239-247, (2013).

Nano, N. & Houry, W. A. Chaperone-like activity of the AAA+ proteins Rvb1 and Rvb2 in the assembly of various complexes. Philos Trans R Soc Lond B Biol Sci 368, 20110399, (2013).

van der Schot, G., Zhang, Z., Vernon, R., Shen, Y., Vranken, W. F., Baker, D., Bonvin, A. M. & Lange, O. F. Improving 3D structure prediction from chemical shift data. J Biomol NMR 57, 27-35, (2013).

Vernon, R., Shen, Y., Baker, D. & Lange, O. F. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker. J Biomol NMR 57, 117-127, (2013).

2012

Andresen, C., Helander, S., Lemak, A., Fares, C., Csizmok, V., Carlsson, J., Penn, L. Z., Forman- Kay, J. D., Arrowsmith, C. H., Lundstrom, P. & Sunnerhagen, M. Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. Nucleic Acids Res 40, 6353-6366, (2012).

Beharry, A. A., Chen, T., Al-Abdul-Wahid, M. S., Samanta, S., Davidov, K., Sadovski, O., Ali, A. M., Chen, S. B., Prosser, R. S., Chan, H. S. & Woolley, G. A. Quantitative analysis of the effects of photoswitchable distance constraints on the structure of a globular protein. Biochemistry 51, 6421-6431, (2012).

Errington, W. J., Khan, M. Q., Bueler, S. A., Rubinstein, J. L., Chakrabartty, A. & Prive, G. G. Adaptor protein self-assembly drives the control of a cullin-RING ubiquitin ligase. Structure 20, 1141-1153, (2012).

Liang, X., Da Paula, A. C., Bozoky, Z., Zhang, H., Bertrand, C. A., Peters, K. W., Forman-Kay, J. D. & Frizzell, R. A. Phosphorylation-dependent 14-3-3 protein interactions regulate CFTR biogenesis. Mol. Biol. Cell 23, 996-1009, (2012).

Mulvihill, C. M. & Deber, C. M. Structural basis for misfolding at a disease phenotypic position in CFTR: comparison of TM3/4 helix-loop-helix constructs with TM4 peptides. Biochim. Biophys. Acta 1818, 49-54, (2012).

Rabeh, W. M., Bossard, F., Xu, H., Okiyoneda, T., Bagdany, M., Mulvihill, C. M., Du, K., di Bernardo, S., Liu, Y., Konermann, L., Roldan, A. & Lukacs, G. L. Correction of both NBD1 energetics and domain interface is required to restore DeltaF508 CFTR folding and function. Cell 148, 150-163, (2012).

Son, I., Shek, Y. L., Dubins, D. N. & Chalikian, T. V. Volumetric characterization of tri-Nacetylglucosamine binding to lysozyme. Biochemistry 51, 5784-5790, (2012).

Tang, X., Orlicky, S., Mittag, T., Csizmok, V., Pawson, T., Forman-Kay, J. D., Sicheri, F. & Tyers, M. Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase. Proc. Natl. Acad. Sci. U. S. A. 109, 3287-3292,
(2012).

Tulumello, D. V. & Deber, C. M. Efficiency of detergents at maintaining membrane protein structures in their biologically relevant forms. Biochim. Biophys. Acta 1818, 1351-1358, (2012).

Zarrine-Afsar, A., Zhang, Z., Schweiker, K.L., Makhatadze, G.I., Davidson, A.R. & Chan, H.S. Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain. Proteins: Structure, Function, and Bioinformatics 80, 858-870 (2012).

Zhang, Z. & Chan, H.S. Transition paths, diffusive processes, and preequilibria of protein folding. Proceedings of the National Academy of Sciences, USA 109, 20919-20924 (2012).

2011

Avadisian, M., Fletcher, S., Liu, B., Zhao, W., Yue, P., Badali, D., Xu, W., Schimmer, A.D., Turkson, J., Gradinaru, C.C., and Gunning, P.T. Artificially induced protein-membrane anchorage with cholesterol-based recognition agents as a new therapeutic concept. Angewandte Chemie International Ed In English 50, 6248-6253. (2011)

Chan, H.S., Zhang, Z., Wallin, S., and Liu, Z. Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Annual Review of Physical Chemistry 62, 301-326. (2011)
Dias, C.L., Karttunen, M & Chan, H.S. Hydrophobic interactions in the formation of secondary structures in small peptides. Physical Review E 84, 041931 (2011).
Fan, H.Y., Shek, Y.L., Amiri, A., Dubins, D.N., Heerklotz, H., Macgregor, R.B., Jr., and Chalikian, T.V. Volumetric characterization of sodium-induced G-quadruplex formation. Journal of the American Chemical Society 133, 4518-4526. (2011)
Kanjee, U., Gutsche, I., Alexopoulos, E., Zhao, B., El Bakkouri, M., Thibault, G., Liu, K., Ramachandran, S., Snider, J., Pai, E.F., and Houry, W.A. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO Journal 30, 931-944. (2011)
Mazouchi, A., Liu, B., Bahram, A., and Gradinaru, C.C. On the performance of bioanalytical fluorescence correlation spectroscopy measurements in a multiparameter photon-counting microscope. Analytica Chimica Acta 688, 61-69. (2011)
Mulvihill, C.M., and Deber, C.M. Structural basis for misfolding at a disease phenotypic position in CFTR: Comparison of TM3/4 helix-loop-helix constructs with TM4 peptides. Biochimica et Biophysica Acta 1818, 49-54. (2011)
Qiu, W., Zhang, J., Dekker, M.J., Wang, H., Huang, J., Brumell, J.H., and Adeli, K. Hepatic autophagy mediates endoplasmic reticulum stress-induced degradation of misfolded apolipoprotein B. Hepatology 53, 1515-1525. (2011)
Saleem, Q., Liu, B., Gradinaru, C.C., and Macdonald, P.M. Lipogels: single-lipid-bilayer-enclosed hydrogel spheres. Biomacromolecules 12, 2364-2374. (2011)
Shek, Y.L., and Chalikian, T.V. Volumetric characterization of interactions of glycine betaine with protein groups. J Phys Chem B 115, 11481-11489. (2011)
Stocki, P., Wang, X.N., Morris, N.J., and Dickinson, A.M. HSP70 natively and specifically associates with an N-terminal dermcidin-derived peptide that contains an HLA-A*03 antigenic epitope. Journal of Biological Chemistry 286, 12803-12811. (2011)
Tulumello, D.V., and Deber, C.M. Positions of polar amino acids alter interactions between transmembrane segments and detergents. Biochemistry 50, 3928-3935. (2011)

2010

Badali, D., Liu, B., Mazouchi, A., Avadisian, M., Gunning, P.T., & Gradinaru, C.C. Development of STAT3 as an accessible target for fluorescence-based inhibition assays. Journal of Undergraduate Life Sciences 4, 18-23. (2010)

Chan, J., Yamazaki, H., Ishiyama, N., Seo, M.D., Mal, T.K., Michikawa, T., Mikoshiba, K., and Ikura, M. Structural studies of inositol 1,4,5-trisphosphate receptor: coupling ligand binding to channel gating. Journal of Biological Chemistry 285, 36092-36099. (2010)
Clark, G.W., and Tillier, E.R. Loss and gain of GroEL in the Mollicutes. Biochemistry and Cell Biology 88, 185-194. (2010)
Craig, D.B., Haslam, A.M., Coombs, J.M., and Nichols, E.R. Kinetic studies of unmodified individual Escherichia coli beta-galactosidase molecules in free solution. Biochemistry and Cell Biology 88, 451-458. (2010)
Craig, D.B., Haslam, A.M., Silverstein, H.J., Chikamatsu, M., Shadabi, E., and Nichols, E.R. Effect of size, quaternary structure and translational error on the static and dynamic heterogeneity of beta-galactosidase and measurement of electrophoretic dynamic heterogeneity. Protein J 29, 398-406. (2010)
El Bakkouri, M., Gutsche, I., Kanjee, U., Zhao, B., Yu, M., Goret, G., Schoehn, G., Burmeister, W.P., and Houry, W.A. Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity. Proc Natl Acad Sci U S A 107, 22499-22504. (2010)
El Bakkouri, M., Pow, A., Mulichak, A., Cheung, K.L., Artz, J.D., Amani, M., Fell, S., de Koning-Ward, T.F., Goodman, C.D., McFadden, G.I., Ortega, J., Hui, R., and Houry, W.A. The Clp chaperones and proteases of the human malaria parasite Plasmodium falciparum. J Mol Biol 404, 456-477. (2010)
Fatemi, N., Korzhnev, D.M., Velyvis, A., Sarkar, B., and Forman-Kay, J.D. NMR characterization of copper-binding domains 4-6 of ATP7B. Biochemistry 49, 8468-8477. (2010)
Hansen, D.F., Neudecker, P., Vallurupalli, P., Mulder, F.A., and Kay, L.E. Determination of Leu side-chain conformations in excited protein states by NMR relaxation dispersion. Journal of the American Chemical Society 132, 42-43. (2010)
Kerman, A., Liu, H.N., Croul, S., Bilbao, J., Rogaeva, E., Zinman, L., Robertson, J., and Chakrabartty, A. Amyotrophic lateral sclerosis is a non-amyloid disease in which extensive misfolding of SOD1 is unique to the familial form. Acta Neuropathol 119, 335-344. (2010)
Khan, M.Q., Sweeting, B., Mulligan, V.K., Arslan, P.E., Cashman, N.R., Pai, E.F., and Chakrabartty, A. Prion disease susceptibility is affected by beta-structure folding propensity and local side-chain interactions in PrP. Proceedings of the National Academy of Sciences of the United States of America 107, 19808-19813. (2010)
Kimber, M.S., Yu, A.Y., Borg, M., Leung, E., Chan, H.S., and Houry, W.A. Structural and theoretical studies indicate that the cylindrical protease ClpP samples extended and compact conformations. Structure 18, 798-808. (2010)
Kozlov, G., Pocanschi, C.L., Rosenauer, A., Bastos-Aristizabal, S., Gorelik, A., Williams, D.B., and Gehring, K. Structural basis of carbohydrate recognition by calreticulin. Journal of Biological Chemistry 285, 38612-38620. (2010)
Lee, S., Heerklotz, H., and Chalikian, T.V. Effects of buffer ionization in protein transition volumes. Biophysical Chemistry 148, 144-147. (2010)
Lee, S., Shek, Y.L., and Chalikian, T.V. Urea interactions with protein groups: a volumetric study. Biopolymers 93, 866-879. (2010)
Liu, B., Mazouchi, A., and Gradinaru, C.C. Trapping single molecules in liposomes: surface interactions and freeze-thaw effects. J Phys Chem B 114, 15191-15198. (2010)
MacKinnon, N., Guerin, G., Liu, B., Gradinaru, C.C., Rubinstein, J.L., and Macdonald, P.M. Triggered instability of liposomes bound to hydrophobically modified core-shell PNIPAM hydrogel beads. Langmuir 26, 1081-1089. (2010)
McLean, J., Liu, H.N., Miletic, D., Weng, Y.C., Rogaeva, E., Zinman, L., Kriz, J., and Robertson, J. Distinct biochemical signatures characterize peripherin isoform expression in both traumatic neuronal injury and motor neuron disease. Journal of Neurochemistry 114, 1177-1192. (2010)
Mulvihill, C.M., and Deber, C.M. Evidence that the translocon may function as a hydropathy partitioning filter. Biochimica et Biophysica Acta 1798, 1995-1998. (2010)
Ng, D.P., and Deber, C.M. Modulation of the oligomerization of myelin proteolipid protein by transmembrane helix interaction motifs. Biochemistry 49, 6896-6902. (2010)
Ng, D.P., and Deber, C.M. Deletion of a terminal residue disrupts oligomerization of a transmembrane alpha-helix. Biochemistry and Cell Biology 88, 339-345. (2010)
Stocki, P., Morris, N.J., Preisinger, C., Wang, X.N., Kolch, W., Multhoff, G., and Dickinson, A.M. Identification of potential HLA class I and class II epitope precursors associated with heat shock protein 70 (HSPA). Cell Stress and Chaperones 15, 729-741. (2010)
Sweeting, B., Khan, M.Q., Chakrabartty, A., and Pai, E.F. Structural factors underlying the species barrier and susceptibility to infection in prion disease. Biochemistry and Cell Biology 88, 195-202. (2010)
Wang, H., Wei, E., Quiroga, A.D., Sun, X., Touret, N., and Lehner, R. Altered lipid droplet dynamics in hepatocytes lacking triacylglycerol hydrolase expression. Molecular Biology of the Cell 21, 1991-2000. (2010)
Zhang, F., Timm, K.A., Arndt, K.M., and Woolley, G.A. Photocontrol of coiled-coil proteins in living cells. Angewandte Chemie International Ed In English 49, 3943-3946. (2010)
Zhang, Z., and Chan, H.S. Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins. Proceedings of the National Academy of Sciences of the United States of America 107, 2920-2925. (2010)

2009

Badasyan, A., Liu, Z.R., and Chan, H.S. Interplaying Roles of Native Topology and Chain Length in Marginally Cooperative and Noncooperative Folding of Small Protein Fragments. International Journal of Quantum Chemistry 109, 3482-3499. (2009)
Baldwin, A.J., Hansen, D.F., Vallurupalli, P., and Kay, L.E. Measurement of methyl axis orientations in invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. Journal of the American Chemical Society 131, 11939-11948. (2009)
Chan, H.S., and Zhang, Z. Liaison amid disorder: non-native interactions may underpin long-range coupling in proteins. J Biol 8, 27. (2009)
Ferguson, A., Liu, Z., and Chan, H.S. Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins. Journal of Molecular Biology 389, 619-636. (2009)
Glozman, R., Okiyoneda, T., Mulvihill, C.M., Rini, J.M., Barriere, H., and Lukacs, G.L. N-glycans are direct determinants of CFTR folding and stability in secretory and endocytic membrane traffic. Journal of Cell Biology 184, 847-862. (2009)
Gong, Y., Kakihara, Y., Krogan, N., Greenblatt, J., Emili, A., Zhang, Z., and Houry, W.A. An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol 5, 275. (2009)
Hansen, D.F., Vallurupalli, P., and Kay, L.E. Measurement of methyl group motional parameters of invisible, excited protein states by NMR spectroscopy. Journal of the American Chemical Society 131, 12745-12754. (2009)
Kahr, W.H., Savoia, A., Pluthero, F.G., Li, L., Christensen, H., De Rocco, D., Traivaree, C., Butchart, S.E., Curtin, J., Stollar, E.J., Forman-Kay, J.D., and Blanchette, V.S. Megakaryocyte and platelet abnormalities in a patient with a W33C mutation in the conserved SH3-like domain of myosin heavy chain IIA. Thrombosis and Haemostasis 102, 1241-1250. (2009)
Korzhnev, D.M., Bezsonova, I., Lee, S., Chalikian, T.V., and Kay, L.E. Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy. Journal of Molecular Biology 386, 391-405. (2009)
Lee, S., and Chalikian, T.V. Volumetric properties of solvation in binary solvents. J Phys Chem B 113, 2443-2450. (2009)
Lin, S.L., Zarrine-Afsar, A., and Davidson, A.R. The osmolyte trimethylamine-N-oxide stabilizes the Fyn SH3 domain without altering the structure of its folding transition state. Protein Science 18, 526-536. (2009)
Liu, B., Fletcher, S., Avadisian, M., Gunning, P.T., and Gradinaru, C.C. A photostable, pH-invariant fluorescein derivative for single-molecule microscopy. J Fluoresc 19, 915-920. (2009)
Liu, H.N., Sanelli, T., Horne, P., Pioro, E.P., Strong, M.J., Rogaeva, E., Bilbao, J., Zinman, L., and Robertson, J. Lack of evidence of monomer/misfolded superoxide dismutase-1 in sporadic amyotrophic lateral sclerosis. Annals of Neurology 66, 75-80. (2009)
Lundstrom, P., Hansen, D.F., Vallurupalli, P., and Kay, L.E. Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy. Journal of the American Chemical Society 131, 1915-1926. (2009)
Lundstrom, P., Vallurupalli, P., Hansen, D.F., and Kay, L.E. Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy. Nat Protoc 4, 1641-1648. (2009)
MacKinnon, N., Guerin, G., Liu, B., Gradinaru, C.C., and Macdonald, P.M. Liposome-hydrogel bead complexes prepared via biotin-avidin conjugation. Langmuir 25, 9413-9423. (2009)
Mao, X., Li, X., Sprangers, R., Wang, X., Venugopal, A., Wood, T., Zhang, Y., Kuntz, D.A., Coe, E., Trudel, S., Rose, D., Batey, R.A., Kay, L.E., and Schimmer, A.D. Clioquinol inhibits the proteasome and displays preclinical activity in leukemia and myeloma. Leukemia 23, 585-590. (2009)
Murphy, J.M., Hansen, D.F., Wiesner, S., Muhandiram, D.R., Borg, M., Smith, M.J., Sicheri, F., Kay, L.E., Forman-Kay, J.D., and Pawson, T. Structural studies of FF domains of the transcription factor CA150 provide insights into the organization of FF domain tandem arrays. Journal of Molecular Biology 393, 409-424. (2009)
Rath, A., Tulumello, D.V., and Deber, C.M. Peptide models of membrane protein folding. Biochemistry 48, 3036-3045. (2009)
Sadovski, O., Beharry, A.A., Zhang, F., and Woolley, G.A. Spectral tuning of azobenzene photoswitches for biological applications. Angewandte Chemie International Ed In English 48, 1484-1486. (2009)
Stollar, E.J., Garcia, B., Chong, P.A., Rath, A., Lin, H., Forman-Kay, J.D., and Davidson, A.R. Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p. Journal of Biological Chemistry 284, 26918-26927. (2009)
Tulumello, D.V., and Deber, C.M. SDS micelles as a membrane-mimetic environment for transmembrane segments. Biochemistry 48, 12096-12103. (2009)
Vallurupalli, P., Hansen, D.F., Lundstrom, P., and Kay, L.E. CPMG relaxation dispersion NMR experiments measuring glycine 1H alpha and 13C alpha chemical shifts in the 'invisible' excited states of proteins. Journal of Biomolecular NMR 45, 45-55. (2009)
Zhang, F., Zarrine-Afsar, A., Al-Abdul-Wahid, M.S., Prosser, R.S., Davidson, A.R., and Woolley, G.A. Structure-based approach to the photocontrol of protein folding. Journal of the American Chemical Society 131, 2283-2289. (2009)
Zhang, Y., Kozlov, G., Pocanschi, C.L., Brockmeier, U., Ireland, B.S., Maattanen, P., Howe, C., Elliott, T., Gehring, K., and Williams, D.B. ERp57 does not require interactions with calnexin and calreticulin to promote assembly of class I histocompatibility molecules, and it enhances peptide loading independently of its redox activity. Journal of Biological Chemistry 284, 10160-10173. (2009)
Zhang, Z., and Chan, H.S. Native topology of the designed protein Top7 is not conducive to cooperative folding. Biophysical Journal 96, L25-27. (2009)
Zinman, L., Liu, H.N., Sato, C., Wakutani, Y., Marvelle, A.F., Moreno, D., Morrison, K.E., Mohlke, K.L., Bilbao, J., Robertson, J., and Rogaeva, E. A mechanism for low penetrance in an ALS family with a novel SOD1 deletion. Neurology 72, 1153-1159. (2009)

2008

Alasti, F., Sadeghi, A., Sanati, M.H., Farhadi, M., Stollar, E., Somers, T., and Van Camp, G. A mutation in HOXA2 is responsible for autosomal-recessive microtia in an Iranian family. Am J Hum Genet 82, 982-991. (2008)

Alexopoulos, E., Kanjee, U., Snider, J., Houry, W.A., and Pai, E.F. Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 64, 700-706. (2008)
Badasyan, A., Liu, Z., and Chan, H.S. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues. Journal of Molecular Biology 384, 512-530. (2008)
Bai, Y., Markham, K., Chen, F., Weerasekera, R., Watts, J., Horne, P., Wakutani, Y., Bagshaw, R., Mathews, P.M., Fraser, P.E., Westaway, D., St George-Hyslop, P., and Schmitt-Ulms, G. The in vivo brain interactome of the amyloid precursor protein. Mol Cell Proteomics 7, 15-34. (2008)
Bai, Y., Markham, K., Chen, F., Weerasekera, R., Watts, J., Horne, P., Wakutani, Y., Bagshaw, R., Mathews, P.M., Fraser, P.E., Westaway, D., St George-Hyslop, P., and Schmitt-Ulms, G. The in vivo brain interactome of the amyloid precursor protein. Mol Cell Proteomics 7, 15-34. (2008)
Bezsonova, I., Bruce, M.C., Wiesner, S., Lin, H., Rotin, D., and Forman-Kay, J.D. Interactions between the three CIN85 SH3 domains and ubiquitin: implications for CIN85 ubiquitination. Biochemistry 47, 8937-8949. (2008)
Bezsonova, I., Forman-Kay, J., and Prosser, R.S. Molecular oxygen as a paramagnetic NMR probe of protein solvent exposure and topology. Concepts in Magnetic Resonance Part A 32A, 239-253. (2008)
Chen, J.M., Ren, H., Shaw, J.E., Wang, Y.J., Li, M., Leung, A.S., Tran, V., Berbenetz, N.M., Kocincova, D., Yip, C.M., Reyrat, J.M., and Liu, J. Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein. Nucleic Acids Res 36, 2123-2135. (2008)
Deber, C.M., Cheung, J.C., and Rath, A. Defining the defect in F508 del CFTR: a soluble problem? Chemistry and Biology 15, 3-4. (2008)
Gribun, A., Cheung, K.L., Huen, J., Ortega, J., and Houry, W.A. Yeast Rvb1 and Rvb2 are ATP-dependent DNA helicases that form a heterohexameric complex. Journal of Molecular Biology 376, 1320-1333. (2008)
Hansen, D.F., Vallurupalli, P., and Kay, L.E. Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states. Journal of Biomolecular NMR 41, 113-120. (2008)
Hansen, D.F., Vallurupalli, P., and Kay, L.E. Quantifying two-bond 1HN-13CO and one-bond 1H(alpha)-13C(alpha) dipolar couplings of invisible protein states by spin-state selective relaxation dispersion NMR spectroscopy. Journal of the American Chemical Society 130, 8397-8405. (2008)
Hansen, D.F., Vallurupalli, P., and Kay, L.E. An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins. J Phys Chem B 112, 5898-5904. (2008)
Hansen, D.F., Vallurupalli, P., Lundstrom, P., Neudecker, P., and Kay, L.E. Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do? Journal of the American Chemical Society 130, 2667-2675. (2008)
Korzhnev, D.M., and Kay, L.E. Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding. Acc Chem Res 41, 442-451. (2008)
Lee, S., Tikhomirova, A., Shalvardjian, N., and Chalikian, T.V. Partial molar volumes and adiabatic compressibilities of unfolded protein states. Biophysical Chemistry 134, 185-199. (2008)
Lum, R., Niggemann, M., and Glover, J.R. Peptide and protein binding in the axial channel of Hsp104. Insights into the mechanism of protein unfolding. Journal of Biological Chemistry 283, 30139-30150. (2008)
Lundstrom, P., Hansen, D.F., and Kay, L.E. Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively (13)C labeled samples. Journal of Biomolecular NMR 42, 35-47. (2008)
McLean, J., Xiao, S., Miyazaki, K., and Robertson, J. A novel peripherin isoform generated by alternative translation is required for normal filament network formation. Journal of Neurochemistry 104, 1663-1673. (2008)
Rath, A., and Deber, C.M. Surface recognition elements of membrane protein oligomerization. Proteins 70, 786-793. (2008)
Sprangers, R., Li, X., Mao, X., Rubinstein, J.L., Schimmer, A.D., and Kay, L.E. TROSY-based NMR evidence for a novel class of 20S proteasome inhibitors. Biochemistry 47, 6727-6734. (2008)
Taulier, N., and Chalikian, T.V. Gamma-cyclodextrin forms a highly compressible complex with 1-adamantanecarboxylic acid. J Phys Chem B 112, 9546-9549. (2008)
Vallurupalli, P., Hansen, D.F., and Kay, L.E. Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 105, 11766-11771. (2008)
Vallurupalli, P., Hansen, D.F., and Kay, L.E. Probing structure in invisible protein states with anisotropic NMR chemical shifts. Journal of the American Chemical Society 130, 2734-2735. (2008)
Xiao, S., Sato, C., Kawarai, T., Goodall, E.F., Pall, H.S., Zinman, L.H., Robertson, J., Morrison, K., and Rogaeva, E. Genetic studies of GRN and IFT74 in amyotrophic lateral sclerosis. Neurobiology of Aging 29, 1279-1282. (2008)
Xiao, S., Tjostheim, S., Sanelli, T., McLean, J.R., Horne, P., Fan, Y., Ravits, J., Strong, M.J., and Robertson, J. An aggregate-inducing peripherin isoform generated through intron retention is upregulated in amyotrophic lateral sclerosis and associated with disease pathology. Journal of Neuroscience 28, 1833-1840. (2008)
Zarrine-Afsar, A., Wallin, S., Neculai, A.M., Neudecker, P., Howell, P.L., Davidson, A.R., and Chan, H.S. Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding. Proceedings of the National Academy of Sciences of the United States of America 105, 9999-10004. (2008)
Zhang, F., Sadovski, O., and Woolley, G.A. Synthesis and characterization of a long, rigid photoswitchable cross-linker for promoting peptide and protein conformational change. Chembiochem 9, 2147-2154. (2008)
Zhao, R., Kakihara, Y., Gribun, A., Huen, J., Yang, G., Khanna, M., Costanzo, M., Brost, R.L., Boone, C., Hughes, T.R., Yip, C.M., and Houry, W.A. Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. Journal of Cell Biology 180, 563-578. (2008)

2007

Bezsonova, I., Evanics, F., Marsh, J.A., Forman-Kay, J.D., and Prosser, R.S. Oxygen as a paramagnetic probe of clustering and solvent exposure in folded and unfolded states of an SH3 domain. Journal of the American Chemical Society 129, 1826-1835. (2007)

Borg, M., Mittag, T., Pawson, T., Tyers, M., Forman-Kay, J.D., and Chan, H.S. Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. Proceedings of the National Academy of Sciences of the United States of America 104, 9650-9655. (2007)
Burns, D.C., Zhang, F., and Woolley, G.A. Synthesis of 3,3'-bis(sulfonato)-4,4'-bis(chloroacetamido)azobenzene and cysteine cross-linking for photo-control of protein conformation and activity. Nat Protoc 2, 251-258. (2007)
Evanics, F., Kitevski, J.L., Bezsonova, I., Forman-Kay, J., and Prosser, R.S. 19F NMR studies of solvent exposure and peptide binding to an SH3 domain. Biochimica et Biophysica Acta 1770, 221-230. (2007)
Haynes, J., Garcia, B., Stollar, E.J., Rath, A., Andrews, B.J., and Davidson, A.R. The biologically relevant targets and binding affinity requirements for the function of the yeast actin-binding protein 1 Src-homology 3 domain vary with genetic context. Genetics 176, 193-208. (2007)
Korzhnev, D.M., Religa, T.L., Lundstrom, P., Fersht, A.R., and Kay, L.E. The folding pathway of an FF domain: characterization of an on-pathway intermediate state under folding conditions by (15)N, (13)C(alpha) and (13)C-methyl relaxation dispersion and (1)H/(2)H-exchange NMR spectroscopy. Journal of Molecular Biology 372, 497-512. (2007)
Lundstrom, P., Teilum, K., Carstensen, T., Bezsonova, I., Wiesner, S., Hansen, D.F., Religa, T.L., Akke, M., and Kay, L.E. Fractional 13C enrichment of isolated carbons using [1-13C]- or [2- 13C]-glucose facilitates the accurate measurement of dynamics at backbone Calpha and side-chain methyl positions in proteins. Journal of Biomolecular NMR 38, 199-212. (2007)
Markham, K., Bai, Y., and Schmitt-Ulms, G. Co-immunoprecipitations revisited: an update on experimental concepts and their implementation for sensitive interactome investigations of endogenous proteins. Anal Bioanal Chem 389, 461-473. (2007)
Murphy, J.M., Korzhnev, D.M., Ceccarelli, D.F., Briant, D.J., Zarrine-Afsar, A., Sicheri, F., Kay, L.E., and Pawson, T. Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain. Proceedings of the National Academy of Sciences of the United States of America 104, 14336-14341. (2007)
Rath, A., and Deber, C.M. Membrane protein assembly patterns reflect selection for non-proliferative structures. FEBS Letters 581, 1335-1341. (2007)
Rath, A., Johnson, R.M., and Deber, C.M. Peptides as transmembrane segments: decrypting the determinants for helix-helix interactions in membrane proteins. Biopolymers 88, 217-232. (2007)
Robertson, J., Sanelli, T., Xiao, S., Yang, W., Horne, P., Hammond, R., Pioro, E.P., and Strong, M.J. Lack of TDP-43 abnormalities in mutant SOD1 transgenic mice shows disparity with ALS. Neuroscience Letters 420, 128-132. (2007)
Sanelli, T., Xiao, S., Horne, P., Bilbao, J., Zinman, L., and Robertson, J. Evidence that TDP-43 is not the major ubiquitinated target within the pathological inclusions of amyotrophic lateral sclerosis. Journal of Neuropathology and Experimental Neurology 66, 1147-1153. (2007)
Sprangers, R., and Kay, L.E. Probing supramolecular structure from measurement of methyl (1)H-(13)C residual dipolar couplings. Journal of the American Chemical Society 129, 12668-12669. (2007)
Sprangers, R., and Kay, L.E. Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445, 618-622. (2007)
Sprangers, R., Velyvis, A., and Kay, L.E. Solution NMR of supramolecular complexes: providing new insights into function. Nat Methods 4, 697-703. (2007)
Tugarinov, V., Sprangers, R., and Kay, L.E. Probing side-chain dynamics in the proteasome by relaxation violated coherence transfer NMR spectroscopy. Journal of the American Chemical Society 129, 1743-1750. (2007)
Vallurupalli, P., Hansen, D.F., Stollar, E., Meirovitch, E., and Kay, L.E. Measurement of bond vector orientations in invisible excited states of proteins. Proceedings of the National Academy of Sciences of the United States of America 104, 18473-18477. (2007)
Vallurupalli, P., Scott, L., Williamson, J.R., and Kay, L.E. Strong coupling effects during X-pulse CPMG experiments recorded on heteronuclear ABX spin systems: artifacts and a simple solution. Journal of Biomolecular NMR 38, 41-46. (2007)
Weerasekera, R., She, Y.M., Markham, K.A., Bai, Y., Opalka, N., Orlicky, S., Sicheri, F., Kislinger, T., and Schmitt-Ulms, G. Interactome and interface protocol (2IP): a novel strategy for high sensitivity topology mapping of protein complexes. Proteomics 7, 3835-3852. (2007)
Wehbi, H., Rath, A., Glibowicka, M., and Deber, C.M. Role of the extracellular loop in the folding of a CFTR transmembrane helical hairpin. Biochemistry 46, 7099-7106. (2007)
Zhang, F., Sadovski, O., Xin, S.J., and Woolley, G.A. Stabilization of folded peptide and protein structures via distance matching with a long, rigid cross-linker. Journal of the American Chemical Society 129, 14154-14155. (2007)
Zhuravleva, A., Korzhnev, D.M., Nolde, S.B., Kay, L.E., Arseniev, A.S., Billeter, M., and Orekhov, V.Y. Propagation of dynamic changes in barnase upon binding of barstar: an NMR and computational study. Journal of Molecular Biology 367, 1079-1092. (2007)

2006

Bezsonova, I., Korzhnev, D.M., Prosser, R.S., Forman-Kay, J.D., and Kay, L.E. Hydration and packing along the folding pathway of SH3 domains by pressure-dependent NMR. Biochemistry 45, 4711-4719. (2006)

Choi, J., Chiang, A., Taulier, N., Gros, R., Pirani, A., and Husain, M. A calmodulin-binding site on cyclin E mediates Ca2+-sensitive G1/s transitions in vascular smooth muscle cells. Circulation Research 98, 1273-1281. (2006)
Eli, P., and Chakrabartty, A. Variants of DsRed fluorescent protein: Development of a copper sensor. Protein Science 15, 2442-2447. (2006)
Evanics, F., Bezsonova, I., Marsh, J., Kitevski, J.L., Forman-Kay, J.D., and Prosser, R.S. Tryptophan solvent exposure in folded and unfolded states of an SH3 domain by 19F and 1H NMR. Biochemistry 45, 14120-14128. (2006)
Go, M.Y., Kim, S., Partridge, A.W., Melnyk, R.A., Rath, A., Deber, C.M., and Mogridge, J. Self-association of the transmembrane domain of an anthrax toxin receptor. Journal of Molecular Biology 360, 145-156. (2006)
Johnson, R.M., Rath, A., and Deber, C.M. The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity. Biochemistry and Cell Biology 84, 1006-1012. (2006)
Johnson, R.M., Rath, A., Melnyk, R.A., and Deber, C.M. Lipid solvation effects contribute to the affinity of Gly-xxx-Gly motif-mediated helix-helix interactions. Biochemistry 45, 8507-8515. (2006)
Korzhnev, D.M., Bezsonova, I., Evanics, F., Taulier, N., Zhou, Z., Bai, Y., Chalikian, T.V., Prosser, R.S., and Kay, L.E. Probing the transition state ensemble of a protein folding reaction by pressure-dependent NMR relaxation dispersion. Journal of the American Chemical Society 128, 5262-5269. (2006)
Korzhnev, D.M., Neudecker, P., Zarrine-Afsar, A., Davidson, A.R., and Kay, L.E. Abp1p and Fyn SH3 domains fold through similar low-populated intermediate states. Biochemistry 45, 10175-10183. (2006)
Neudecker, P., Korzhnev, D.M., and Kay, L.E. Assessment of the effects of increased relaxation dispersion data on the extraction of 3-site exchange parameters characterizing the unfolding of an SH3 domain. Journal of Biomolecular NMR 34, 129-135. (2006)
Rath, A., Melnyk, R.A., and Deber, C.M. Evidence for assembly of small multidrug resistance proteins by a "two-faced" transmembrane helix. Journal of Biological Chemistry 281, 15546-15553. (2006)
Reichheld, S.E., and Davidson, A.R. Two-way interdomain signal transduction in tetracycline repressor. Journal of Molecular Biology 361, 382-389. (2006)
Snider, J., Gutsche, I., Lin, M., Baby, S., Cox, B., Butland, G., Greenblatt, J., Emili, A., and Houry, W.A. Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase. Journal of Biological Chemistry 281, 1532-1546. (2006)
Snider, J., and Houry, W.A. MoxR AAA+ ATPases: a novel family of molecular chaperones? Journal of Structural Biology 156, 200-209. (2006)
Taulier, N., and Chalikian, T.V. Hydrophobic hydration in cyclodextrin complexation. J Phys Chem B 110, 12222-12224. (2006)
Thibault, G., Tsitrin, Y., Davidson, T., Gribun, A., and Houry, W.A. Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone. EMBO Journal 25, 3367-3376. (2006)
Tikhomirova, A., Beletskaya, I.V., and Chalikian, T.V. Stability of DNA duplexes containing GG, CC, AA, and TT mismatches. Biochemistry 45, 10563-10571. (2006)
Vallurupalli, P., and Kay, L.E. Complementarity of ensemble and single-molecule measures of protein motion: a relaxation dispersion NMR study of an enzyme complex. Proceedings of the National Academy of Sciences of the United States of America 103, 11910-11915. (2006)
Vallurupalli, P., Scott, L., Hennig, M., Williamson, J.R., and Kay, L.E. New RNA labeling methods offer dramatic sensitivity enhancements in 2H NMR relaxation spectra. Journal of the American Chemical Society 128, 9346-9347. (2006)
Wallin, S., and Chan, H.S. Conformational entropic barriers in topology-dependent protein folding: perspectives from a simple native-centric polymer model. Journal of Physics-Condensed Matter 18, S307-S328. (2006)
Woolley, G.A., Lee, E.S., and Zhang, F. sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking. Bioinformatics 22, 3101-3102. (2006)
Xiao, S., McLean, J., and Robertson, J. Neuronal intermediate filaments and ALS: a new look at an old question. Biochimica et Biophysica Acta 1762, 1001-1012. (2006)
Zhang, F., and Berti, P.J. Phosphate analogues as probes of the catalytic mechanisms of MurA and AroA, two carboxyvinyl transferases. Biochemistry 45, 6027-6037. (2006)
Zhang, Y., Baig, E., and Williams, D.B. Functions of ERp57 in the folding and assembly of major histocompatibility complex class I molecules. Journal of Biological Chemistry 281, 14622-14631. (2006)

2005

Bezsonova, I., Singer, A., Choy, W.Y., Tollinger, M., and Forman-Kay, J.D. Structural comparison of the unstable drkN SH3 domain and a stable mutant. Biochemistry 44, 15550-15560. (2005)

Borg, M., Stampfl, C., Mikkelsen, A., Gustafson, J., Lundgren, E., Scheffler, M., and Andersen, J.N. Density of configurational states from first-principles calculations: the phase diagram of Al-Na surface alloys. Chemphyschem 6, 1923-1928. (2005)
Eisenmesser, E.Z., Millet, O., Labeikovsky, W., Korzhnev, D.M., Wolf-Watz, M., Bosco, D.A., Skalicky, J.J., Kay, L.E., and Kern, D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 438, 117-121. (2005)
Gribun, A., Kimber, M.S., Ching, R., Sprangers, R., Fiebig, K.M., and Houry, W.A. The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. Journal of Biological Chemistry 280, 16185-16196. (2005)
Han, F., Taulier, N., and Chalikian, T.V. Association of the minor groove binding drug Hoechst 33258 with d(CGCGAATTCGCG)2: volumetric, calorimetric, and spectroscopic characterizations. Biochemistry 44, 9785-9794. (2005)
Korzhnev, D.M., Mittermaier, A.K., and Kay, L.E. Cross-correlated spin relaxation effects in methyl 1H CPMG-based relaxation dispersion experiments: complications and a simple solution. Journal of Biomolecular NMR 31, 337-342. (2005)
Korzhnev, D.M., Neudecker, P., Mittermaier, A., Orekhov, V.Y., and Kay, L.E. Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: an application to the folding of a Fyn SH3 domain mutant. Journal of the American Chemical Society 127, 15602-15611. (2005)
Korzhnev, D.M., Orekhov, V.Y., and Kay, L.E. Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock fields: an application to a Fyn SH3 domain. Journal of the American Chemical Society 127, 713-721. (2005)
Mittermaier, A., Korzhnev, D.M., and Kay, L.E. Side-chain interactions in the folding pathway of a Fyn SH3 domain mutant studied by relaxation dispersion NMR spectroscopy. Biochemistry 44, 15430-15436. (2005)
Rath, A., Davidson, A.R., and Deber, C.M. The structure of "unstructured" regions in peptides and proteins: role of the polyproline II helix in protein folding and recognition. Biopolymers 80, 179-185. (2005)
Sprangers, R., Gribun, A., Hwang, P.M., Houry, W.A., and Kay, L.E. Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release. Proceedings of the National Academy of Sciences of the United States of America 102, 16678-16683. (2005)
Taulier, N., Beletskaya, I.V., and Chalikian, T.V. Compressibility changes accompanying conformational transitions of apomyoglobin. Biopolymers 79, 218-229. (2005)
Vallurupalli, P., and Kay, L.E. A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics. Journal of the American Chemical Society 127, 6893-6901. (2005)
Wallin, S., and Chan, H.S. A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling. Protein Science 14, 1643-1660. (2005)

2004

Di Nardo, A.A., Korzhnev, D.M., Stogios, P.J., Zarrine-Afsar, A., Kay, L.E., and Davidson, A.R. Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation. Proceedings of the National Academy of Sciences of the United States of America 101, 7954-7959. (2004)

Korzhnev, D.M., Kloiber, K., Kanelis, V., Tugarinov, V., and Kay, L.E. Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme. Journal of the American Chemical Society 126, 3964-3973. (2004)
Korzhnev, D.M., Kloiber, K., and Kay, L.E. Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application. Journal of the American Chemical Society 126, 7320-7329. (2004)
Korzhnev, D.M., Salvatella, X., Vendruscolo, M., Di Nardo, A.A., Davidson, A.R., Dobson, C.M., and Kay, L.E. Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature 430, 586-590. (2004)
Orekhov, V.Y., Korzhnev, D.M., and Kay, L.E. Double- and zero-quantum NMR relaxation dispersion experiments sampling millisecond time scale dynamics in proteins. Journal of the American Chemical Society 126, 1886-1891. (2004)
Tikhomirova, A., Taulier, N., and Chalikian, T.V. Energetics of nucleic acid stability: the effect of DeltaCP. Journal of the American Chemical Society 126, 16387-16394. (2004)
Zhang, K., Quan, C., Huang, H., Taulier, N., and Wu, X.Y. On the stability of insulin delivered through a new glucose-responsive polymeric composite membrane. Journal of Pharmacy and Pharmacology 56, 611-620. (2004)

2003

Kanjilal, S., Taulier, N., Le Huerou, J.Y., Gindre, M., Urbach, W., and Waks, M. Ultrasonic studies of alcohol-induced transconformation in beta-lactoglobulin: the intermediate state. Biophysical Journal 85, 3928-3934. (2003)
Korzhnev, D.M., Orekhov, V.Y., Dahlquist, F.W., and Kay, L.E. Off-resonance R1rho relaxation outside of the fast exchange limit: an experimental study of a cavity mutant of T4 lysozyme. Journal of Biomolecular NMR 26, 39-48. (2003)
Noudeh, G.D., Taulier, N., and Chalikian, T.V. Volumetric characterization of homopolymeric amino acids. Biopolymers 70, 563-574. (2003)
Taulier, N., and Chalikian, T.V. Volumetric effects of ionization of amino and carboxyl termini of alpha,omega-aminocarboxylic acids. Biophysical Chemistry 104, 21-36. (2003)

2002

Korzhnev, D.M., Skrynnikov, N.R., Millet, O., Torchia, D.A., and Kay, L.E. An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. Journal of the American Chemical Society 124, 10743-10753. (2002)
Taulier, N., and Chalikian, T.V. Compressibility of protein transitions. Biochimica et Biophysica Acta 1595, 48-70. (2002)