Heinrich Roder

Summary

Affiliation: Fox Chase Cancer Center
Country: USA

Publications

  1. pmc Stepwise helix formation and chain compaction during protein folding
    Heinrich Roder
    Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Proc Natl Acad Sci U S A 101:1793-4. 2004
  2. ncbi request reprint Rapid mixing methods for exploring the kinetics of protein folding
    Heinrich Roder
    Basic Science Division, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA
    Methods 34:15-27. 2004
  3. pmc Folding kinetics of staphylococcal nuclease studied by tryptophan engineering and rapid mixing methods
    Kosuke Maki
    Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    J Mol Biol 368:244-55. 2007
  4. pmc Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxide
    Ramil F Latypov
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    J Mol Biol 383:437-53. 2008
  5. pmc Solution structure of the A4 domain of factor XI sheds light on the mechanism of zymogen activation
    Dharmaraj Samuel
    Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Proc Natl Acad Sci U S A 104:15693-8. 2007
  6. pmc Early events in protein folding explored by rapid mixing methods
    Heinrich Roder
    Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Chem Rev 106:1836-61. 2006
  7. ncbi request reprint Early events during folding of wild-type staphylococcal nuclease and a single-tryptophan variant studied by ultrarapid mixing
    Kosuke Maki
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    J Mol Biol 338:383-400. 2004
  8. pmc The effects of pK(a) tuning on the thermodynamics and kinetics of folding: design of a solvent-shielded carboxylate pair at the a-position of a coiled-coil
    Wai Leung Lau
    Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
    Biophys J 99:2299-308. 2010
  9. pmc Autoinhibitory interactions between the PDZ2 and C-terminal domains in the scaffolding protein NHERF1
    Hong Cheng
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Structure 17:660-9. 2009
  10. pmc Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein
    Yongjin Zhu
    Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 100:15486-91. 2003

Collaborators

Detail Information

Publications35

  1. pmc Stepwise helix formation and chain compaction during protein folding
    Heinrich Roder
    Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Proc Natl Acad Sci U S A 101:1793-4. 2004
  2. ncbi request reprint Rapid mixing methods for exploring the kinetics of protein folding
    Heinrich Roder
    Basic Science Division, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA
    Methods 34:15-27. 2004
    ..These developments have been especially important for exploring early stages of protein folding...
  3. pmc Folding kinetics of staphylococcal nuclease studied by tryptophan engineering and rapid mixing methods
    Kosuke Maki
    Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    J Mol Biol 368:244-55. 2007
    ....
  4. pmc Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxide
    Ramil F Latypov
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    J Mol Biol 383:437-53. 2008
    ..The thermodynamic and kinetic parameters obtained in this study provide a fully self-consistent description of the linked unfolding/CO binding equilibria of reduced cytochrome c...
  5. pmc Solution structure of the A4 domain of factor XI sheds light on the mechanism of zymogen activation
    Dharmaraj Samuel
    Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Proc Natl Acad Sci U S A 104:15693-8. 2007
    ..The results are consistent with biochemical evidence that activated FXI cleaves its substrate at two positions without release of an intermediate...
  6. pmc Early events in protein folding explored by rapid mixing methods
    Heinrich Roder
    Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Chem Rev 106:1836-61. 2006
  7. ncbi request reprint Early events during folding of wild-type staphylococcal nuclease and a single-tryptophan variant studied by ultrarapid mixing
    Kosuke Maki
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    J Mol Biol 338:383-400. 2004
    ....
  8. pmc The effects of pK(a) tuning on the thermodynamics and kinetics of folding: design of a solvent-shielded carboxylate pair at the a-position of a coiled-coil
    Wai Leung Lau
    Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
    Biophys J 99:2299-308. 2010
    ..By contrast, the doubly charged state shows a reduced rate of folding and a ϕ-value near 0.5 indicative of a repulsive interaction, and possibly also heterogeneity in the transition state ensemble...
  9. pmc Autoinhibitory interactions between the PDZ2 and C-terminal domains in the scaffolding protein NHERF1
    Hong Cheng
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Structure 17:660-9. 2009
    ..The findings provide a structural framework for understanding how autoinhibitory interactions modulated the binding properties of NHERF1...
  10. pmc Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein
    Yongjin Zhu
    Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 100:15486-91. 2003
    ..alpha3D shows a significant bias toward local helical structure in the thermally denatured state. The molecular dynamics-simulated TS ensemble is highly heterogeneous and dynamic, allowing access to the TS via multiple pathways...
  11. ncbi request reprint Structural characterization of an equilibrium unfolding intermediate in cytochrome c
    Ramil F Latypov
    Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    J Mol Biol 357:1009-25. 2006
    ....
  12. pmc Mapping of POP1-binding site on pyrin domain of ASC
    Thiagarajan Srimathi
    Basic Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    J Biol Chem 283:15390-8. 2008
    ..Based on our observations, we propose that the positive EPSP of ASC_PYD, including the H2 and H3 helices, may be the binding site for Cryopyrin, and the interaction with Cryopyrin may induce the dissociation of POP1 from ASC_PYD...
  13. pmc De novo design of a single-chain diphenylporphyrin metalloprotein
    Gretchen M Bender
    Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    J Am Chem Soc 129:10732-40. 2007
    ....
  14. pmc Microsecond folding dynamics of apomyoglobin at acidic pH
    Ming Xu
    Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    J Phys Chem B 116:7014-25. 2012
    ....
  15. pmc Dimer dissociation and unfolding mechanism of coagulation factor XI apple 4 domain: spectroscopic and mutational analysis
    Paul W Riley
    Department of Biochemistry and The Sol Sherry Thrombosis Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA
    J Mol Biol 367:558-73. 2007
    ....
  16. pmc Design of a switchable eliminase
    Ivan V Korendovych
    Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 108:6823-7. 2011
    ..The activity of this minimal 75-residue allosterically regulated catalyst is similar to that obtained using more elaborate computational approaches to redesign complex enzymes to catalyze the Kemp elimination reaction...
  17. pmc Retroviral integrases promote fraying of viral DNA ends
    Richard A Katz
    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    J Biol Chem 286:25710-8. 2011
    ..We conclude that frayed ends represent a functional intermediate in which DNA termini can be sampled for suitability for endonucleolytic processing...
  18. pmc Intrinsic disorder and oligomerization of the hepatitis delta virus antigen
    Carolina Alves
    Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Virology 407:333-40. 2010
    ..Oligomers of purified δAg were resistant to elevated NaCl and urea concentrations, and bound without specificity to RNA and single- and double-stranded DNAs...
  19. ncbi request reprint Structure, stability, and function of hDim1 investigated by NMR, circular dichroism, and mutational analysis
    Yu Zhu Zhang
    Division of Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Biochemistry 42:9609-18. 2003
    ..Other residues essential for hDim1 function are identified by using mutational and genetic approaches. The residues thus identified are not identical with those previously shown to govern Dim1 interaction with defined protein partners...
  20. pmc Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach
    Andreas Lehmann
    a Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA
    MAbs 7:1058-71. 2015
    ..We provide here a novel strategy for redesigning the light chain of problematic scFvs to enhance their stability and therapeutic applicability. ..
  21. pmc Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c
    Hossein Fazelinia
    Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
    J Am Chem Soc 136:733-40. 2014
    ..Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse. ..
  22. ncbi request reprint Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integrase
    Jizu Yi
    Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, Pennsylvania 19111, USA
    J Biol Chem 277:12164-74. 2002
    ....
  23. pmc Arginyltransferase ATE1 catalyzes midchain arginylation of proteins at side chain carboxylates in vivo
    Junling Wang
    Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA
    Chem Biol 21:331-7. 2014
    ..This midchain arginylation implies an unconventional mechanism of ATE1 action that likely facilitates its major biological role. ..
  24. pmc Early intermediate in human prion protein folding as evidenced by ultrarapid mixing experiments
    Adrian C Apetri
    Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, USA
    J Am Chem Soc 128:11673-8. 2006
    ..Overall, the present data strongly suggest that this partially structured intermediate may be a direct monomeric precursor of the misfolded PrP(Sc) oligomer...
  25. pmc Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing
    Kaare Teilum
    Department of Protein Chemistry, Institute of Molecular Biology, University of Copenhagen, DK 1353 Copenhagen K, Denmark
    Proc Natl Acad Sci U S A 99:9807-12. 2002
    ..The findings indicate that ultrafast mixing methods combined with sensitive conformational probes can reveal transient accumulation of intermediate states in proteins with apparent two-state folding mechanisms...
  26. ncbi request reprint Parallel pathways in cytochrome c(551) folding
    Stefano Gianni
    Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche e Istituto di Biologia e Patologia Molecolari del CNR, Universita di Roma La Sapienza, Piazzale A Moro 5, 00185 Rome, Italy
    J Mol Biol 330:1145-52. 2003
    ..These findings indicate the presence of two or more slowly inter-converting ensembles of denatured states that give rise to pH-dependent partitioning among fast and slow-folding pathways...
  27. pmc NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126
    Kazuo Kuwata
    Department of Biochemistry and Biophysics, School of Medicine, Gifu University, 40 Tsukasa Machi, Gifu 500 8705, Japan
    Proc Natl Acad Sci U S A 100:14790-5. 2003
    ..Fibril formation involving polyalanine stacking is consistent with the experimental observations...
  28. ncbi request reprint Effects of heme on the structure of the denatured state and folding kinetics of cytochrome b562
    Pascal Garcia
    Instituto de Quimica Fisica Rocasolano, CSIC, C Serrano, 119, 28006 Madrid, Spain
    J Mol Biol 346:331-44. 2005
    ..These data should be considered in the analysis of folding of heme proteins...
  29. pmc Conformational equilibration time of unfolded protein chains and the folding speed limit
    Christina J Abel
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 46:4090-9. 2007
    ....
  30. pmc Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchange
    William F Walkenhorst
    Department of Chemistry, Loyola University, New Orleans, Louisiana 70118, USA
    Protein Sci 11:82-91. 2002
    ....
  31. ncbi request reprint Internal friction controls the speed of protein folding from a compact configuration
    Suzette A Pabit
    Department of Physics, University of Florida, P O Box 118440, Gainesville, Florida 32611 8440, USA
    Biochemistry 43:12532-8. 2004
    ....
  32. pmc Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A
    Ervin Welker
    Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 1301, USA
    Proc Natl Acad Sci U S A 101:17681-6. 2004
    ..Thus, contrary to previous expectations, the isomerization state of proline peptide bonds can have a major impact on the structural events during early stages of folding...
  33. pmc A cytochrome c mutant with high electron transfer and antioxidant activities but devoid of apoptogenic effect
    Ziedulla Kh Abdullaev
    Laboratory of Spectral Analysis, M M Shemyakin and Y A Ovchinnikov Institute of Bioorganic Chemistry, Moscow 177871, Russia
    Biochem J 362:749-54. 2002
    ....
  34. ncbi request reprint Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome C
    Stephen J Hagen
    Physics Department, University of Florida, P O Box 118440, Gainesville, Florida 32611, USA
    Biochemistry 41:1372-80. 2002
    ..Thus, the stiffness of the polypeptide chain creates a deviation from Gaussian chain behavior by impeding, although not preventing, the formation of short (<10 peptide bonds) intrachain loops around the heme group...
  35. ncbi request reprint Kinetics of loop formation and breakage in the denatured state of iso-1-cytochrome c
    Eydiejo Kurchan
    Department of Chemistry and Biochemistry, 2190 E Iliff Avenue, University of Denver, Denver, CO 80208 2436, USA
    J Mol Biol 353:730-43. 2005
    ..The implications of the kinetics of loop formation and breakage in the denatured state for the mechanism of protein folding are discussed...