Research Topics
Species | H RoderSummaryAffiliation: Fox Chase Cancer Center Country: USA Publications
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Publications
Kinetic role of early intermediates in protein foldingH Roder
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Curr Opin Struct Biol 7:15-28. 1997..Recent spectroscopic studies, coupled with quantitative kinetic analysis, suggest that folding is facilitated by the rapid formation of compact intermediates with some native-like structural features...- Methods for exploring early events in protein foldingH Roder
Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
Curr Opin Struct Biol 9:620-6. 1999.... - Early events in protein folding explored by rapid mixing methodsHeinrich Roder
Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
Chem Rev 106:1836-61. 2006 - Rapid mixing methods for exploring the kinetics of protein foldingHeinrich 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... - Stepwise helix formation and chain compaction during protein foldingHeinrich 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 - Structural and kinetic description of cytochrome c unfolding induced by the interaction with lipid vesiclesT J Pinheiro
Institute for Cancer Research, Fox Chase Cancer Centre, 7701 Burholme Avenue, Philadelphia, Pennsylvania 19111, USA
Biochemistry 36:13122-32. 1997..This lipid-denatured equilibrium state (DL) is clearly more extensively unfolded than the A-state in solution, but is distinct from the unfolded protein in water (UW), which has no stable secondary structure... - Ultrafast folding of alpha3D: a de novo designed three-helix bundle proteinYongjin 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... - Early events during folding of wild-type staphylococcal nuclease and a single-tryptophan variant studied by ultrarapid mixingKosuke Maki
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
J Mol Biol 338:383-400. 2004.... - Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxideRamil 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... - Folding kinetics of staphylococcal nuclease studied by tryptophan engineering and rapid mixing methodsKosuke Maki
Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
J Mol Biol 368:244-55. 2007.... - Structure, stability, and function of hDim1 investigated by NMR, circular dichroism, and mutational analysisYu 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... - De novo design of a single-chain diphenylporphyrin metalloproteinGretchen 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.... - Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integraseJizu Yi
Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, Pennsylvania 19111, USA
J Biol Chem 277:12164-74. 2002.... - The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamilyY Z Zhang
Division of Basic Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
Physiol Genomics 1:109-18. 1999..In sum, this study identifies the Dim1 proteins as a novel sixth branch of the thioredoxin superfamily involved in cell cycle... - Solution structure of the A4 domain of factor XI sheds light on the mechanism of zymogen activationDharmaraj 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... - Mapping of POP1-binding site on pyrin domain of ASCThiagarajan 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... - Dimer dissociation and unfolding mechanism of coagulation factor XI apple 4 domain: spectroscopic and mutational analysisPaul 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.... - Autoinhibitory interactions between the PDZ2 and C-terminal domains in the scaffolding protein NHERF1Hong 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... - Structural characterization of an equilibrium unfolding intermediate in cytochrome cRamil F Latypov
Basic Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
J Mol Biol 357:1009-25. 2006.... - Intrinsic disorder and oligomerization of the hepatitis delta virus antigenCarolina Alves
Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Virology 407:333-40. 2010..Oligomers of purified ?Ag were resistant to elevated NaCl and urea concentrations, and bound without specificity to RNA and single- and double-stranded DNAs... - Conformational equilibration time of unfolded protein chains and the folding speed limitChristina J Abel
Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
Biochemistry 46:4090-9. 2007.... - Effects of heme on the structure of the denatured state and folding kinetics of cytochrome b562Pascal 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... - Early formation of a beta hairpin during folding of staphylococcal nuclease H124L as detected by pulsed hydrogen exchangeWilliam F Walkenhorst
Department of Chemistry, Loyola University, New Orleans, Louisiana 70118, USA
Protein Sci 11:82-91. 2002.... - Early intermediate in human prion protein folding as evidenced by ultrarapid mixing experimentsAdrian 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... - NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126Kazuo 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... - Parallel pathways in cytochrome c(551) foldingStefano Gianni
Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche e Istituto di Biologia e Patologia Molecolari del CNR, , 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... - Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixingKaare 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... - Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome CStephen 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... - A cytochrome c mutant with high electron transfer and antioxidant activities but devoid of apoptogenic effectZiedulla 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.... - Kinetics of loop formation and breakage in the denatured state of iso-1-cytochrome cEydiejo 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... - Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease AErvin 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... - Internal friction controls the speed of protein folding from a compact configurationSuzette A Pabit
Department of Physics, University of Florida, P.O. Box 118440, Gainesville, Florida 32611-8440, USA
Biochemistry 43:12532-8. 2004....
Research Grants
- KINETICS OF EARLY EVENTS IN PROTEIN FOLDINGHeinrich Roder; Fiscal Year: 2009..Studies of protein folding in vitro further provide the necessary framework for protein structure prediction, and for understanding cellular protein folding, trafficking and degradation. ..
- KINETICS OF EARLY EVENTS IN PROTEIN FOLDINGHeinrich Roder; Fiscal Year: 2009..Studies of protein folding in vitro further provide the necessary framework for protein structure prediction, and for understanding cellular protein folding, trafficking and degradation. ..
- KINETICS OF EARLY EVENTS IN PROTEIN FOLDINGHeinrich Roder; Fiscal Year: 2005....
- KINETICS OF EARLY EVENTS IN PROTEIN FOLDINGHeinrich Roder; Fiscal Year: 2001..Roder's laboratory by conventional structural and kinetic methods. The results will provide unique insight into the structural and dynamic properties of early structural intermediates and their kinetic role in protein folding. ..
- KINETICS OF EARLY EVENTS IN PROTEIN FOLDINGHeinrich Roder; Fiscal Year: 2010..Studies of protein folding in vitro further provide the necessary framework for protein structure prediction, and for understanding cellular protein folding, trafficking and degradation. ..