Faculty Summaries
Heinrich Roder, PhD
Heinrich Roder, PhD
Professor
  • Adjunct Professor, University of Pennsylvania
  • Professor, Temple University
  • Director, Spectroscopy Support Facility
Heinrich.Roder@fccc.edu
Office Phone: 215-728-3123
Fax: 215-728-3574
Office: R414
Lab: R407/408

2000 - Present

  • Fazelinia, H., Xu, M., Cheng, H., Roder, H. Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c. J. Am. Chem. Soc., in press. JACS PubMed
  • Montalvo, G. L., Gai, F., Roder, H., Degrado, W. F. Slow Folding-Unfolding Kinetics of an Octameric beta-Peptide Bundle. ACS Chem Biol. 2014; 9:276-81. PubMed
  • Mizukami, T., Xu, M., Cheng, H., Roder, H., Maki, K. Non-uniform chain collapse during early stages of staphylococcal nuclease folding by fluorescence resonance energy transfer and ultrarapid mixing methods. Protein Science 2013; 22:1336-48. PubMed
  • Moroz, O.V., Moroz, Y. S., Wu, Y., Olsen, A. B., Cheng, H., Mack, K. L., McLaughlin, J. M., Raymond, E. A., Zhezherya, K., Roder, H, Korendovych, I. V. A Single Mutation in a Regulatory Protein Produces Evolvable Allosterically Regulated Catalyst of Nonnatural Reaction. Angew. Chem. Int. Ed. Engl. 2013; 52:6246-6249. PubMed
  • Xu M, Beresneva O, Rosario R, Roder H. Microsecond Folding Dynamics of Apomyoglobin at Acidic pH. J Phys Chem B. 2012; 116(23):7014-25. PubMed
  • Korendovych I V, Kulp DW, Wu Y, Cheng H, Roder H, DeGrado WF. Design of a switchable eliminase. Proc Natl Acad Sci U S A. 2011; 108:6823-7. PubMed
  • Chen KC, Xu M, Wedemeyer WJ, Roder H. Microsecond unfolding kinetics of sheep prion protein reveals an intermediate that correlates with susceptibility to classical scrapie. Biophys J. 2011;101:1221-30. PubMed
  • Katz, R. A., Merkel, G., Andrake, M. D., Roder, H. & Skalka, A. M. Retroviral integrases promote fraying of viral DNA ends. J. Biol. Chem.2011; 286:25710-8 PubMed
  • Lau WL, DeGrado WF, Roder H. The effects of pKa tuning on the thermodynamics and kinetics of folding: Design of a solvent-shielded carboxylate pair at the “a”position of a coiled coil. Biophys J. 2010; 99:2299-2308. PubMed
  • Alves C, Cheng H, Roder H, Taylor J. Intrinsic disorder and oligomerization of the hepatitis delta virus antigen. Virology. 2010; 407:333-340. PubMed
  • Cheng H, Li J, Fazlieva R, Dai Z, Bu Z, Roder H. Autoinhibitory interactions between the PDZ2 and C-terminal domains in the scaffolding protein NHERF1. Structure. 2009;17(5):660-669.
  • Tzul FO, Kurchan E, Roder H, Bowler BE. Competition between reversible aggregation and loop formation in denatured iso-1-cytochrome c. Biochemistry. 2009;48(2):481-91.
  • Latypov RF, Maki K, Cheng H, Luck SD, Roder H. Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxide. J Mol Biol. 2008;383(2):437-53.
  • Srimathi T, Robbins SL, Dubas RL, Chang H, Cheng H, Roder H, Park YC. Mapping of POP1-binding site on pyrin domain of ASC. J Biol Chem. 2008;283(22):15390-8.
  • Abel CJ, Goldbeck RA, Latypov RF, Roder H, Kliger DS. Conformational equilibration time of unfolded protein chains and the folding speed limit. Biochemistry. 2007;46(13):4090-9.
  • Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, Degrado WF. De Novo Design of a Single-Chain Diphenylporphyrin Metalloprotein. J Am Chem Soc. 2007;129(35):10732-40.
  • Maki K, Cheng H, Dolgikh DA, Roder H. Folding kinetics of staphylococcal nuclease studied by tryptophan engineering and rapid mixing methods. J Mol Biol. 2007;368(1):244-55.
  • Riley PW, Cheng H, Samuel D, Roder H, Walsh PN. Dimer Dissociation and Unfolding Mechanism of Coagulation Factor XI Apple 4 Domain: Spectroscopic and Mutational Analysis. J Mol Biol. 2007;367(2):558-73.
  • Samuel D, Cheng H, Riley PW, Canutescu AA, Nagaswami C, Weisel JW, Bu Z, Walsh PN, Roder H. Solution structure of the A4 domain of factor XI sheds light on the mechanism of zymogen activation. Proc Natl Acad Sci USA. 2007;104(40):15693-8.
  • Apetri AC, Maki K, Roder H, Surewicz WK. Early intermediate in human prion protein folding as evidenced by ultrarapid mixing experiments. J Am Chem Soc. 2006;128(35):11673-8.
  • Latypov RF, Cheng H, Roder NA, Zhang J, Roder H. Structural characterization of an equilibrium unfolding intermediate in cytochrome c. J Mol Biol. 2006;357(3):1009-25.
  • Roder H, Maki K, Cheng H. Early events in protein folding explored by rapid mixing methods. Chem Rev. 2006;106(5):1836-61.
  • Garcia P, Bruix M, Rico M, Ciofi-Baffoni S, Banci L, Ramachandra Shastry MC, Roder H, de Lumley Woodyear T, Johnson CM, Fersht AR, Barker PD. Effects of Heme on the Structure of the Denatured State and Folding Kinetics of Cytochrome b(562). J Mol Biol. 2005;346(1):331-44.
  • Kurchan E, Roder H, Bowler BE. Kinetics of Loop Formation and Breakage in the Denatured State of Iso-1-cytochrome c. J Mol Biol. 2005;353(3):730-43.
  • Roder H, Maki K, Latypov RF, Cheng H, Shastry MCR. Early events in protein folding explored by rapid mixing methods. In: J Buchner; T Kiefhaber, editors, translator and editor Protein folding handbook. Part I. Weinheim: Wiley-VCH; 2005; p. 491-535.
  • Maki K, Cheng H, Dolgikh DA, Shastry MC, Roder H. Early Events During Folding of Wild-type Staphylococcal Nuclease and a Single-tryptophan Variant Studied by Ultrarapid Mixing. J Mol Biol. 2004;338(2):383-400.
  • Pabit SA, Roder H, Hagen SJ. Internal friction controls the speed of protein folding from a compact configuration. Biochemistry. 2004;43(39):12532-8.
  • Roder H. Stepwise helix formation and chain compaction during protein folding. Proc Natl Acad Sci USA. 2004;101(7):1793-4.
  • Roder H, Maki K, Cheng H, Shastry MC. Rapid mixing methods for exploring the kinetics of protein folding. Methods. 2004;34(1):15-27.
  • Welker E, Maki K, Shastry MC, Juminaga D, Bhat R, Scheraga HA, Roder H. Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A. Proc Natl Acad Sci USA. 2004;101(51):17681-6.
  • Gianni S, Travaglini-Allocatelli C, Cutruzzola F, Brunori M, Shastry MC, Roder H. Parallel pathways in cytochrome c(551) folding. J Mol Biol. 2003;330(5):1145-52.
  • Kuwata K, Matumoto T, Cheng H, Nagayama K, James TL, 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. 2003;100(25):14790-5.
  • Zhang YZ, Cheng H, Gould KL, Golemis EA, Roder H. Structure, Stability, and Function of hDim1 Investigated by NMR, Circular Dichroism, and Mutational Analysis. Biochemistry. 2003;42(32):9609-18.
  • Zhu Y, Alonso DO, Maki K, Huang CY, Lahr SJ, Daggett V, Roder H, DeGrado WF, Gai F. Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein. Proc Natl Acad Sci USA. 2003;100(26):15486-91.
  • Abdullaev Z, Bodrova ME, Chernyak BV, Dolgikh DA, Kluck RM, Pereverzev MO, Arseniev AS, Efremov RG, Kirpichnikov MP, Mokhova EN, Newmeyer DD, Roder H et al. A cytochrome c mutant with high electron transfer and antioxidant activities but devoid of apoptogenic effect. Biochem J. 2002;362(Pt 3):749-54.
  • Hagen SJ, Latypov RF, Dolgikh DA, Roder H. Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome C. Biochemistry 2002;41(4):1372-80.
  • Teilum K, Maki K, Kragelund BB, Poulsen FM, Roder H. Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing. Proc Natl Acad Sci USA. 2002;99(15):9807-12.
  • Walkenhorst WF, Edwards JA, Markley JL, Roder H. Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange. Protein Sci. 2002;11(1):82-91.
  • Yi J, Cheng H, Andrake MD, Dunbrack RL, Jr., Roder H, Skalka AM. Mapping the epitope of an inhibitory mAb to the C-terminal DNA binding domain of HIV-1 integrase. J Biol Chem. 2002;277(14):12164-74.
  • Capaldi AP, Shastry RMC, Kleanthous C, Roder H, Radford SE. Ultra-rapid mxing experiments reveal that Im7 folds via an on-pathway intermediate. Nat Struct Biol. 2001;8:68-72.
  • Cheng RP, Suich DJ, Cheng H, Roder H, DeGrado WF. Template-constrained somatostatin analogues: a biphenyl linker induces a type-V' turn. J Am Chem Soc. 2001;123(50):12710-1.
  • Kuwata K, Shastry R, Cheng H, Hoshino M, Batt CA, Goto Y, Roder H. Structural and kinetic characterization of early folding events in beta- lactoglobulin. Nat Struct Biol. 2001;8(2):151-5.
  • Latypov RF, Dolgikh DA, Kirpichnikov MP, Ptitsyn OB, Roder H. [Y97V substitution in the horse cytochrome c causes accumulation of the equilibrium intermediate]. Biofizika. 2001 46(1):46-52.
  • Pinheiro TJ, Cheng H, Seeholzer SH, Roder H. Direct evidence for the cooperative unfolding of cytochrome c in lipid membranes from 1H-2H exchange kinetics. J Mol Biol. 2000;303(4):617-26.
  • Roder H, El�ve GA, Shastry RMC. Early stages of protein folding. In: RH Pain, editor, translator and editor Mechanisms of protein folding. New York: Oxford University Press; 2000; p. 65-104.
  • Talaga DS, Lau WL, Roder H, Tang J, Jia Y, DeGrado WF, Hochstrasser RM. Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy. Proc Natl Acad Sci USA. 2000;97(24):13021-6.
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1990 - 1999

  • Park S-H, Shastry MCR, Roder H. Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing. Nat Struct Biol. 1999;6(10):943-7.
  • Rankin SE, Watts A, Roder H, Pinheiro TJT. Folding of apocytochrome c induced by the interaction with negatively charged lipid micelles proceeds via a collapsed intermediate state. Protein Science. 1999;8(2).
  • Roder H, Shastry MCR. Methods for exploring early events in protein folding. Curr Opin Struct Biol. 1999;9:620-6.
  • Roder H, Shastry MCR, Sauder JM, Park S-H, editors. Kinetic and structural characterization of early events in protein folding Amsterdam: Elsevier; 1999. 65-74 p. (K Kuwajima; M Arai editors. Old and new views of protein folding).
  • Walsh STR, Cheng H, Bryson JW, Roder H, DeGrado WF. Solution structure and dynamics of a de novo designed three helix bundle protein. Proc Natl Acad Sci USA. 1999;96:5486-91.
  • Zhang Y-Z, Gould KL, Dunbrack RL, Jr., Cheng H, Roder H, Golemis EA. The evolutionarily conserved Dim 1 protein defines a novel branch of the thioredoxin fold superfamily. Physiol Genomics. 1999;1:109-18.
  • Dolgikh DA, Latypov RF, Abdullaev ZK, Colon W, Roder H, Kirpichnikov MP. Expression of mutant horse cytochrome c genes in Escherichia coli. Bioorg Khim. 1998;24(10):756-9.
  • Houry WA, Sauder JM, Roder H, Scheraga HA. Definition of amide protection factors for early kinetic intermediates in protein folding. Proc Natl Acad Sci USA. 1998;95:4299-302.
  • Milne JS, Mayne L, Roder H, Wand AJ, Englander SW. Determinants of protein hydrogen exchange studied in equine cytochrome c. Protein Science. 1998;7:739-45.
  • Sauder JM, Roder H. Amide protection in an early folding intermediate of cytochrome c. Folding and Design. 1998;3:293-301.
  • Shastry MCR, Luck SD, Roder H. A continuous-flow capillary mixer to monitor reactions on the microsecond time scale. Biophys J. 1998;74(5):2714-21.
  • Shastry MCR, Roder H. Evidence for barrier-limited protein folding kinetics on the microsecond time scale. Nat Struct Biol. 1998;5:385-92.
  • Shastry MCR, Sauder JM, Roder H. Kinetic and structural analysis of submillisecond folding events in cytochrome c. Acc Chem Res. 1998;31:717-25.
  • Colón W, Wakem LP, Sherman F, Roder H. Identification of the predominant non-native histidine ligand in unfolded cytochrome c. Biochemistry. 1997;36:12535-41.
  • Park S-H, O'Neil KT, Roder H. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core. Biochemistry. 1997;36:14277-83.
  • Pinheiro TJT, Elove GA, Watts A, Roder H. Structural and kinetic description of cytochrome c unfolding induced by the interaction with lipid vesicles. Biochemistry. 1997;36:13122-32.
  • Roder H, Colón W. Kinetic role of early intermediates in protein folding. Curr Opin Struct Biol. 1997;7:15-28.
  • Walkenhorst WF, Green SM, Roder H. Kinetic evidence for folding and unfolding intermediates in Staphylococcal nuclease. Biochemistry. 1997;63:5795-805.
  • Colón W, Elöve GA, Wakem LP, 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;35:5538-49.
  • Colón W, Roder H. Kinetic intermediates in the formation of the cytochrome c molten globule. Nat Struct Biol. 1996;3:1019-25.
  • Khorasanizadeh S, Peters ID, Roder H. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nat Struct Biol. 1996;3(2):193-205.
  • Sauder JM, MacKenzie NE, Roder H. Kinetic mechanism of folding and unfolding of Rhodobacter capsulatus cytochrome c2. Biochemistry. 1996;35:16852-62.
  • Gochin M, Roder H. Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cyochrome c. Protein Science. 1995;4:296-305.
  • Laub PB, Khorasanizadeh S, Roder H. Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints. Protein Science. 1995;4(May):973-82.
  • Roder H. Watching protein folding unfold. Nat Struct Biol. 1995;2(10):817-20.
  • Zhang Y-Z, Paterson Y, Roder H. Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR. Protein Science. 1995;4(april):804-14.
  • Elöve GA, Bhuyan AK, Roder H. Kinetic mechanism of cytochrome c folding: involvement of the heme and its ligands. Biochemistry. 1994;33(June 7,22):6925-35.
  • Roder H, Elöve GA. Early stages of protein folding. In: RH Pain, editor, translator and editor Mechanisms of Protein Folding: Frontiers in Molecular Biology. New York: Oxford University Press; 1994; p. 26-55.
  • Jones CM, Henry ER, Hu Y, Chan C-K, Luck SD, Bhuyan A, Roder H, Hofrichter J, Eaton WA. Fast events in protein folding initiated by nanosecond laser photolysis. Proc Natl Acad Sci USA. 1993;90(Dec 93):11860-4.
  • Khorasanizadeh S, Peters ID, Butt TR, Roder H. Folding and stability of a tryptophan-containing mutant of ubiquitin. Biochemistry. 1993;32:7054-63.
  • Moore KS, Wehrli S, Roder H, Rogers M, Forrest JN, Mc Crimmon D, Zasloff M. Squalamine An Aminosterol antibiotic from the shark. Proc Natl Acad Sci USA. 1993;90(Feb 15, 4):1354-8.
  • Wehrli SL, Moore KS, Roder H, Durell S, Zasloff M. Structure of the novel steroidal antibiotic squalamine determined by 2-dimensional NMR spectroscopy. Steroids. 1993;58(8,Aug):370-8.
  • Wu L, Laub PB, Elöve GA, Carey J, Roder H. A Noncovalent peptide complex as a model for an early folding intermediate of cytochrome c. Biochemistry. 1993; 32(Sept 28):10271-6.
  • Briggs MS, Roder H. Early hydrogen-bonding events in the folding reaction of ubiquitin. Proc Natl Acad Sci USA. 1992;89:2017-21.
  • Elöve GA, Chaffotte AF, Roder H, Goldberg ME. Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy. Biochemistry. 1992;31:6876-83.
  • Baldwin RL, Roder H. Characterizing protein folding intermediates. Current Biology. 1991;1:218-20.
  • Bhuyan AK, Elöve GA, Roder H. Redox effects on protein stability and folding kinetics of horse cytochrome c. J Cell Biochem. 1991;15G:188.
  • Elöve GA, Roder H. Structure and stability of cytochrome c folding intermediates. ACS Symp Ser. 1991;470:50-63.
  • Feng Y, Roder H, Englander SW. Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c. Biochemistry. 1990;29:3494-504.
  • Feng YQ, Roder H, Englander SW. Assignment of paramagnetically shifted resonances in the 1H NMR spectrum of horse ferricytochrome c. Biophys J. 1990;57(1):15-22.
  • Jeng M-F, Englander SW, Elöve GA, Wand AJ, Roder H. Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry. 1990;29:10433-7.
  • Paterson Y, Englander SW, Roder H. An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR. Science. 1990;249:755.
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1980 - 1989

  • Feng Y, Roder H, Englander SW, Wand AJ, Di Stefano DL. Proton resonance assignments of horse ferricytochrome c. Biochemistry. 1989;28:195-203.
  • Roder H. Structural characterization of protein folding intermediates by proton magnetic resonance and hydrogen exchange. Methods Enzymol. 1989;176:446-73.
  • Wand AJ, Di Stefano DL, Feng Y, Roder H, Englander SW. Proton resonance assignments of horse ferrocytochrome c. Biochemistry. 1989;28:186-94.
  • Englander JJ, Englander SW, Louie G, Roder H, T. T, Wand AJ. Protein Hydrogen Exchange, Dynamics, and Energetics. In: RHSaMH Sarma, editor, translator and editor From Proteins to Ribosomes. Vol. 1: Adenine Press; 1988; p. 107-17.
  • Feng Y, Roder H. Relayed magnetization transfer by isotropic mixing in exchanging systems. J. Magn. Reson. 1988;78:597-602.
  • Roder H, Elöve GA, Englander SW. Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature. 1988;335:700-4.
  • Day EP, Kent TA, Lindahl PA, Munck E, Orme-Johnson WH, Roder H, Roy A. SQUID measurement of metalloprotein magnetization. New methods applied to the nitrogenase proteins. Biophys J. 1987;52(5):837-53.
  • Ansari A, DiIorio EE, Dlott DD, Frauenfelder H, Iben IE, Langer P, Roder H, Sauke TB, Shyamsunder E. Ligand binding to heme proteins: relevance of low-temperature data. Biochemistry. 1986;25(11):3139-46.
  • Roder H, Wand AJ, Milne JS, Englander SW. Effect of methionine ligation on the structural dynamics of cytochrome c studied by 2D NMR observation of amide proton exchange. Biophys J. 1986;49:57a.
  • Wand AJ, Roder H, Englander SW. Two-dimensional 1H NMR studies of cytochrome c: Hydrogen exchange in the N-terminal helix. Biochemistry. 1986;25:1107-14.
  • Roder H, Wüthrich K. Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons. Proteins: Struct Funct Genet. 1986;1:34-42.
  • Chang CH, Govindjee R, Ebrey T, Bagley KA, Dollinger G, Eisenstein L, Marque J, Roder H, Vittitow J, Fang JM, et al. Trans/13-cis isomerization is essential for both the photocycle and proton pumping of bacteriorhodopsin. Biophys J. 1985;47 (4):509-12.
  • Roder H, Wagner G, Wüthrich K. Amide proton exchange in proteins, by EX1 kinetics: Studies of the basic pancreatic trypsin inhibitor at variable p2H and temperature. Biochemistry. 1985;24:7396-407.
  • Roder H, Wagner G, Wüthrich K. Individual amide proton exchange rates in thermally unfolded basic pancreatic trypsin inhibitor. Biochemistry. 1985;24:7407-11.
  • Roder H, Berendzen J, Bowne SF, Frauenfelder H, Sauke TB, Shyamsunder E, Weissman MB. Comparison of the magnetic properties of deoxy- and photodissociated myoglobin. Proc Natl Acad Sci USA. 1984;81(8):2359-63.
  • Dlott DD, Frauenfelder H, Langer P, Roder H, DiIorio EE. Nanosecond flash photolysis study of carbon monoxide binding to the beta chain of hemoglobin Zurich [beta 63(E7)His leads to Arg]. Proc Natl Acad Sci USA. 1983;80(20):6239-43.
  • Wüthrich K, Roder H, Wagner G. Internal Mobility and Unfolding of Globular Proteins. In: R Jaenicke, editor, translator and editor Protein Folding. Amsterdam: Elsevier/North Holland Biomedical Press; 1980; p. 549-64.
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