Selected Publications

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Cheng, H., Li, J., Fazlieva, R., Dai, Z., Bu, Z. & Roder, H. (2009). Autoinhibitory Interactions between the PDZ2 and C-terminal Domains in the Scaffolding Protein NHERF1. Structure 17, 660-669. (pdf)

Tzul, F.O., Kurchan, E., Roder, H., and Bowler, B.E. (2009). Competition between reversible aggregation and loop formation in denatured iso-1-cytochrome c. Biochemistry 48, 481-491. (pdf)

Latypov, R.F., Maki, K., Cheng, H., Luck, S.D., and Roder, H. (2008). Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxide. J. Mol. Biol. 383, 437-453. (pdf)

Srimathi, T., Robbins, S.L., Dubas, R.L., Chang, H., Cheng, H., Roder, H., and Park, Y.C. (2008). Mapping of POP1-binding site on pyrin domain of ASC. J. Biol. Chem. 283, 15390-15398. (pdf)

D. Samuel, H. Cheng, P. W. Riley, A. A. Canutescu, C. Nagaswami, J. W. Weisel, Z. Bu, P. N. Walsh, and H. Roder (2007) Solution structure of the A4 domain of factor XI sheds light on the mechanism of zymogen activation. Proc. Natl. Acad. Sci. USA, 104:15693-98. (pdf)

Bender, G.M., Lehmann, A., Zou, H., Cheng, H., Fry, H.C., Engel, D., Therien, M.J., Blasie, J.K., Roder, H., Saven, J.G., and Degrado, W.F. (2007). De Novo Design of a Single-Chain Diphenylporphyrin Metalloprotein. J. Am. Chem. Soc. 129:10732-10740. (pdf)

Maki, K., Cheng, H., Dolgikh, D. A. & Roder, H. (2007) Folding kinetics of staphylococcal nuclease studied by tryptophan engineering and rapid mixing methods. J. Mol. Biol., 368:244-255. (pdf)

Abel, C.J., Goldbeck, R.A., Latypov, R.F., Roder, H., & Kliger, D.S. (2007) Conformational equilibration time of unfolded protein chains and the folding speed limit. Biochemistry, 46:4090-4099. (pdf)

Riley, P. W., Cheng, H., Samuel, D., Roder, H. & Walsh, P. N. (2007). Dimer Dissociation and Unfolding Mechanism of Coagulation Factor XI Apple 4 Domain: Spectroscopic and Mutational Analysis. J. Mol. Biol. 367:558-573. (pdf)

Apetri, A. C., Maki, K., Roder, H. & Surewicz, W. K. (2006) Early intermediate in human prion protein folding as evidenced by ultrarapid mixing experiments. J. Am. Chem. Soc. 128:11673-8. (pdf)

Roder, H., Maki,K. & Cheng, H. (2006). Early events in protein folding explored by rapid mixing methods. Chem. Rev. 106(5): 1836-1861. (pdf)

Latypov, R. F., Cheng, H., Roder, N. A., Zhang, J. & Roder, H. (2006). Structural Characterization of an Equilibrium Unfolding Intermediate in Cytochrome c. J. Mol. Biol. 357:1009-1025 (pdf)

Kurchan, E., Roder, H. & Bowler, B.E. (2005) Kinetics of Loop Formation and Breakage in the Denatured State of Iso-1-cytochrome c. J. Mol. Biol. 353:730-43. (pdf)

Roder, H., Maki, K., Latypov, R. F., Cheng, H. & Shastry, M. C. R. (2005). Early events in protein folding explored by rapid mixing methods. In Protein Foldign Handbook, Vol. Part I, pp. 491-535. Wiley-VCH, Weinheim. (pdf)

Garcia, P., Bruix, M., Rico, M., Ciofi-Baffoni, S., Banci, L., Ramachandra Shastry, M. C., Roder, H., de Lumley Woodyear, T., Johnson, C. M., Fersht, A. R., et al. (2005). Effects of Heme on the Structure of the Denatured State and Folding Kinetics of Cytochrome b(562). J. Mol. Biol. 346, 331-344. (pdf)

Welker, E., Maki, K., Shastry, M. C., Juminaga, D., Bhat, R., Scheraga, H. A. & Roder, H. (2004). Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A. Proc Natl Acad Sci U S A. 101:17681-17686. (pdf)

Roder, H., Maki, K., Cheng, H. and Shastry, M. C. (2004) Rapid mixing methods for exploring the kinetics of protein folding. Methods 34:15-27. (pdf)

Pabit, S. A., Roder, H. and Hagen, S. J. (2004) Internal friction controls the speed of protein folding from a compact configuration. Biochemistry 43, 12532-12538 (pdf)

Maki, K., Cheng, H., Dolgikh, D. A., Shastry, M. C. & Roder, H. (2004). Early Events During Folding of Wild-type Staphylococcal Nuclease and a Single-tryptophan Variant Studied by Ultrarapid Mixing. J. Mol. Biol. 338, 383-400. (pdf)

Roder, H. (2004). Stepwise helix formation and chain compaction during protein folding. Proc. Natl. Acad. Sci. USA 101, 1793-1794. (pdf) 

Zhu, Y., Alonso, D.O.V., Maki, K., Cheng-Yen Huang, C.-Y., Lahr, S.J., Daggett, V., Roder, H., DeGrado, W.F. & Gai, F. (2003) Ultrafast folding of a3D, a de novo designed three-helix bundle protein. Proc. Natl. Acad. Sci. USA 100, 15486-91. (pdf)

Kuwata, K., Matumoto, T., Cheng, H., Nagayama, K., James, T. L. & Roder, H. NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126. Proc. Natl. Acad. Sci. USA 100, 14790-14795, 2003.

Gianni S, Travaglini-Allocatelli C, Cutruzzola F, Brunori M, Shastry MC, Roder H. Parallel Pathways in Cytochrome c(551) Folding. J. Mol. Biol. 330, 1145-1152, 2003.

Teilum, K., K., Maki, K., Kragelund, B.B., Poulsen, F.M. & Roder, H. Early kinetic intermediate in the folding of Acyl-Coenzyme A Binding Protein detected by fluorescence labeling and ultra rapid mixing. Proc. Natl. Acad. Sci. USA 99, 9807-12, 2002.

Abdullaev, Z., Bodrova, M.E., Chernyak, B.V., Dolgikh, D.A., Kluck, R.M., Pereverzev, M.O., Arseniev, A.S., Efremov, R.G., Kirpichnikov, M.P., Mokhova, E.N., Newmeyer, D.D., Roder, H. & Skulachev, V.P. A cytochrome c mutant with high electron transfer and antioxidant activities but devoid of apoptogenic effect. Biochem J 362, 749-54, 2002.

Yi, J., Cheng, H., Andrake, M.D., Dunbrack, R.L., Jr., Roder, H. & Skalka, A.M. Mapping the epitope of an inhibitory mAb to the C-terminal DNA binding domain of HIV-1 integrase. J. Biol. Chem. 277, 12164-12174, 2002.

Hagen, S.J., Latypov, R.F., Dolgikh, D.A. & Roder, H. Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome c. Biochemistry 41, 1372-80, 2002.

Walkenhorst, W.F., Edwards, J.A., Markley, J.L. & Roder, H. Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange. Protein Sci 11, 82-91, 2002.

Cheng, R.P., Suich, D.J., Cheng, H., Roder, H. & DeGrado, W.F. Template-constrained somatostatin analogues: a biphenyl linker induces a type-V' turn. J. Am. Chem. Soc. 123, 12710-1, 2001.

Kuwata, K., Shastry, M. C. R., Cheng, H., Hoshima, M., Batt, C. A., Goto, Y., & Roder, H. Structural and kinetic characterization of early folding events in b-lactoglobulin. Nature Struct. Biol., 8:151-155, 2001.

Capaldi, A.P., Shastry, M.C.R., Kleanthous, C., Roder, H. & Radford, S.E. Ultra-rapid mixing experiments reveal that Im7 folds via an on-pathway intermediate. Nature Struct. Biol., 8:68-72, 2001.

Talaga, D. S., Lau, W. L., Roder, H., Tang, J., Jia, Y., DeGrado, W. F. & Hochstrasser, R. M. Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy. PNAS, 2000. 97:13021-6.

Pinheiro, T.J., Cheng, H., Seeholzer, S.H. & Roder, H. Direct evidence for the cooperative unfolding of cytochrome c in lipid membranes from H-(2)H exchange kinetics. J. Mol. Biol, 2000. 303:617-26.

Roder, H., Elöve, G.A. & Shastry, M.C.R. Early stages of protein folding. in Protein folding: Frontiers in Molecular Biology (ed. Pain, R.H.) Oxford University Press, New York, 2000. pp. 65-104.

Walsh, S.T.R., Cheng, H., Bryson, J.W., Roder, H. & DeGrado, W.F. Solution structure and dynamics of a de novo designed three helix bundle protein. PNAS, 1999. 96:5486-5491.

Roder, H., Shastry, M.C.R., Sauder, J.M. & Park, S.-H. (Kuwajima, K., Arai, M., eds.). Kinetic and structural characterization of early events in protein folding, 65-74 (Elsevier, Amsterdam, 1999).

Roder, H. & M.C.R. Shastry. Methods for exploring early events in protein folding. Curr. Opin. Struct. Biol., 1999. 9:620-626.

Park, S-H., Shastry, M.C.R. & Roder, H. Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing. Nature Struct. Biol., 1999. 6:943-947.

Rankin, S.E., Watts, A., Roder, H. & Pinheiro, T.J.T. Folding of apocytochrome c induced by the interaction with negatively charged lipid micelles proceeds via a collapsed intermediate state. Protein Science, 1999. 8:381-393.

Sauder, J.M. & Roder, H. Amide protection in an early folding intermediate of cytochrome c. Folding & Design, 1998. 3:293-301.

Shastry, M.C.R., Sauder, J.M. & Roder, H. Kinetic and structural analysis of submillisecond folding events in cytochrome c. Accts. Chem. Res., 1998. 31:717-725.

Shastry, M.C.R. & Roder, H. Evidence for barrier-limited protein folding kinetics on the microsecond time scale. Nature Struct. Biol., 1998. 5: 385-392.

Houry, W.A., Sauder, J.M., Roder, H., and Scheraga, H.A. Definition of amide protection factors for early kinetic intermediates in protein folding. PNAS, 1998. 95: 4299-4302. (PDF)

Shastry, M.C.R., Luck, S.D., and Roder, H. A continuous-flow capillary mixer to monitor reactions on the microsecond time scale. Biophys. J., 1998. 74: 2714-2721. (PDF)

Milne, J.S., Mayne, L., Roder, H., Wand, A.J., and Englander, S.W. Determinants of protein hydrogen exchange studied in equine cytochrome c. Protein Science, 1998. 7: 739-745.

Park, S-H., O'Neil, K. T., and Roder, H. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core. Biochemistry, 1997. 36: 14277-14283.

Pinheiro, T. J. T., Elöve, G. A., Watts, A., and Roder, H. Structural and kinetic description of cytochrome c unfolding induced by the interaction with lipid vesicles. Biochemistry, 1997. 36: 13122-13132.

Colón, W., Wakem, L.P., Sherman, F., Roder, H. Identification of the predominant non-native histidine ligand in unfolded cytochrome c. Biochemistry, 1997. 36: 12535-12541.

Walkenhorst, W. F., Green, S. M., and Roder, H. Kinetic evidence for folding and unfolding intermediates in Staphylococcal nuclease. Biochemistry, 1997. 36: 5795-5805.

Roder, H. and Colón. Kinetic role of early intermediates in protein folding (Review) Current Opinion in Struct. Biology, 1997. 7: 15-28.

Sauder, J. M., MacKenzie, N. E., and Roder, H. Kinetic mechanism of folding and unfolding of Rhodobacter capsulatus cytochrome c2. Biochemistry, 1996. 35: 16852-16862. (PDF)

Colón, W. and Roder, H. Kinetic intermediates in the formation of the cytochrome c molten globule. Nature Struct. Biology, 1996. 3: 1019-1025.

Colón, W., Elöve, G.A., Wakem, L.P., Sherman, F., Roder, H. Side chain packing of the N- and C-terminal helices plays a critical role in the kinetics of cytochrome c folding. Biochemistry, 1996. 35: 5538-5549. (PDF)

Khorasanizadeh, S., Peters, I.D., and Roder, H. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nature Structural Biology, 1996. 3: 193-205.

Roder, H., Watching protein folding unfold. Nature Structural Biology, 1995. 2: 817-820.

Laub, P.B., S. Khorasanizadeh, and H. Roder, Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints. Protein Science, 1995. 4: 973-982.

Zhang, Y.-Z., Y. Paterson, and H. Roder, Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR. Protein Science, 1995. 4: 804-814.

Gochin, M. and H. Roder, Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cyochrome c. Protein Science, 1995. 4: 296-305.

Elöve, G.A., A.K. Bhuyan, and H. Roder, Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands. Biochemistry, 1994. 33: 6925-6935.

Roder, H. and G.A. Elöve, Early stages of protein folding, in Mechanisms of Protein Folding: Frontiers in Molecular Biology, R.H. Pain, Editor. 1994, Oxford University Press: New York. p. 26-55.

Khorasanizadeh, S., Peters, I.D., Butt, T.R., and Roder, H. Stability and folding of a tryptophan-containing mutant of ubiquitin. Biochemistry, 1993. 32: 7054-7063.

Moore, K.S., et al., Squalamine An Aminosterol antibiotic from the shark. Proceedings of the National Academy of Sciences USA, 1993. 90: 1354-1358.

Wu, L., Laub, P.B., Elöve, G.A., Carey, J., and Roder, H. A Noncovalent peptide complex as a model for an early folding intermediate of cytochrome c. Biochemistry, 1993. 32: 10271-10276.

Jones, C.M., Henry, E.R., Hu, Y., Chan, C-K., Luck, S.D., Bhuyan, A., Roder, H., Hofrichter, J., Eaton, W.A. Fast events in protein folding initiated by nanosecond laser photolysis. Proceedings of the National Academy of Sciences USA, 1993. 90: 11860-11864.

Elöve, G.A., Chaffotte, A.F., Roder, H., Goldberg, M.E. Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy. Biochemistry, 1992. 31: 6876-6883.

Briggs, M.S. and H. Roder, Early hydrogen-bonding events in the folding reaction of ubiquitin. Proceedings of the National Academy of Sciences USA, 1992. 89: 2017-2021.

Baldwin, R.L. and H. Roder, Characterizing protein folding intermediates. Current Biology, 1991. 1: 218-220.

Elöve, G.A. and H. Roder, Structure and stability of cytochrome c folding intermediates. ACS Symposium Series, 1991. 470: 50-63.

Jeng, M.-F., Englander, S.W., Elöve, G.A., Wand, A.J., Roder, H. Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry, 1990. 29: 10433-10437.

Feng, Y., H. Roder, and S.W. Englander, Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c. Biochemistry, 1990. 29: 3494-3504.

Paterson, Y., S.W. Englander, and H. Roder, An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR. Science, 1990. 249: 755-759.

Roder, H., Structural characterization of protein folding intermediates by proton magnetic resonance and hydrogen exchange. Methods in Enzymology, 1989. 176: 446-473.

Feng, Y., Roder, H., Englander, S.W., Wand, A.J., Di Stefano, D.L. Proton resonance assignments of horse ferricytochrome c. Biochemistry, 1989. 28: 195-203.

Wand, A.J., Di Stefano, D.L., Feng, Y., Roder, H., Englander, S.W. Proton resonance assignments of horse ferrocytochrome c. Biochemistry, 1989. 28: 186-194.

Feng, Y. and H. Roder, Relayed magnetization transfer by isotropic mixing in exchanging systems. Journal of Magnetic Resonance, 1988. 78: 597-602.

Roder, H., G.A. Elöve, and S.W. Englander, Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature, 1988. 335: 700-704.

Roder, H. and K. Wüthrich, Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons. Proteins: Structure, Function, and Genetics, 1986. 1: 34-42.

Wand, A.J., H. Roder, and S.W. Englander, Two-dimensional 1H NMR studies of cytochrome c: Hydrogen exchange in the N-terminal helix. Biochemistry, 1986. 25: 1107-1114.

Roder, H., G. Wagner, and K. Wüthrich, Individual amide proton exchange rates in thermally unfolded basic pancreatic trypsin inhibitor. Biochemistry, 1985. 24: 7407-7411.

Roder, H., G. Wagner, and K. Wüthrich, Amide proton exchange in proteins, by EX1 kinetics: Studies of the basic pancreatic trypsin inhibitor at variable p2H and temperature. Biochemistry, 1985. 24: 7396-7407.


 

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