Research Output 2003 2017

  • 883 Citations
  • 14 h-Index from Scopus
  • 28 Article
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Article
2017
1 Citations

Functional tuning of the catalytic residue pKa in a de novo designed esterase

Hiebler, K., Lengyel, Z., Castañeda, C. A. & Makhlynets, O. V. 2017 (Accepted/In press) In : Proteins: Structure, Function and Bioinformatics.

Research output: Research - peer-reviewArticle

Esterases
Histidine
Tuning
Electrostatics
Static Electricity
2016
12 Citations

Linkage-specific conformational ensembles of non-canonical polyubiquitin chains

Castañeda, C. A., Chaturvedi, A., Camara, C. M., Curtis, J. E., Krueger, S. & Fushman, D. 2016 In : Physical Chemistry Chemical Physics. 18, 8, p. 5771-5788 18 p.

Research output: Research - peer-reviewArticle

Polyubiquitin
linkages
Lysine
Conformations
Crystal structure
12 Citations

Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins

Castañeda, C. A., Dixon, E. K., Walker, O., Chaturvedi, A., Nakasone, M. A., Curtis, J. E., Reed, M. R., Krueger, S., Cropp, T. A. & Fushman, D. Mar 1 2016 In : Structure. 24, 3, p. 423-436 14 p.

Research output: Research - peer-reviewArticle

Polyubiquitin
Ubiquitin
Lysine
Ubiquitins
Small Angle Scattering
2015
9 Citations

Base-CP proteasome can serve as a platform for stepwise lid formation

Yu, Z., Livnat-Levanon, N., Kleifeld, O., Mansour, W., Nakasone, M. A., Castaneda, C. A., Dixon, E. K., Fushman, D., Reis, N., Pick, E. & Glickman, M. H. 2015 In : Bioscience Reports. 35, e00194

Research output: Research - peer-reviewArticle

Proteasome Endopeptidase Complex
ATP dependent 26S protease
Holoenzymes
Eukaryota
Peptide Hydrolases
14 Citations

DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin

Nowicka, U., Zhang, D., Walker, O., Krutauz, D., Castañeda, C. A., Chaturvedi, A., Chen, T. Y., Reis, N., Glickman, M. H. & Fushman, D. Mar 3 2015 In : Structure. 23, 3, p. 542-557 16 p.

Research output: Research - peer-reviewArticle

Ubiquitin
DNA Damage
Proteins
Saccharomyces cerevisiae Proteins
Protein Transport
3 Citations

Engineered domain swapping as an on/off switch for protein function

Ha, J. H., Karchin, J. M., Walker-Kopp, N., Castañeda, C. A. & Loh, S. N. Oct 22 2015 In : Chemistry and Biology. 22, 10, p. 1384-1393 10 p.

Research output: Research - peer-reviewArticle

Ribose
Carrier Proteins
Switches
Proteins
Ubiquitin
3 Citations

Unexpected Trypsin Cleavage at Ubiquitinated Lysines

Burke, M. C., Wang, Y., Lee, A. E., Dixon, E. K., Castaneda, C. A., Fushman, D. & Fenselau, C. Aug 18 2015 In : Analytical Chemistry. 87, 16, p. 8144-8148 5 p.

Research output: Research - peer-reviewArticle

Ubiquitin
Trypsin
Lysine
Peptides
Polyubiquitin
2014
11 Citations

Alanine scan of core positions in ubiquitin reveals links between dynamics, stability, and function

Lee, S. Y., Pullen, L., Virgil, D. J., Castañeda, C. A., Abeykoon, D., Bolon, D. N. A. & Fushman, D. Apr 3 2014 In : Journal of Molecular Biology. 426, 7, p. 1377-1389 13 p.

Research output: Research - peer-reviewArticle

Ubiquitin
Alanine
Mutation
Proteins
Yeasts
6 Citations

Preparing to read the ubiquitin code: A middle-out strategy for characterization of all lysine-linked diubiquitins

Lee, A. E., Castañeda, C. A., Wang, Y., Fushman, D. & Fenselau, C. 2014 In : Journal of Mass Spectrometry. 49, 12, p. 1272-1278 7 p.

Research output: Research - peer-reviewArticle

Ubiquitin
Lysine
Mass spectrometry
Polyubiquitin
Proteins
9 Citations

Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein

Robinson, A. C., Castañeda, C. A., Schlessman, J. L. & Bertrand García-Moreno, E. Aug 12 2014 In : Proceedings of the National Academy of Sciences of the United States of America. 111, 32, p. 11685-11690 6 p.

Research output: Research - peer-reviewArticle

Burial
Thermodynamics
Ions
Proteins
Micrococcal Nuclease
2013
16 Citations

Modifying the vicinity of the isopeptide bond to reveal differential behavior of ubiquitin chains with interacting proteins: Organic chemistry applied to synthetic proteins

Haj-Yahya, N., Haj-Yahya, M., Castañeda, C. A., Spasser, L., Hemantha, H. P., Jbara, M., Penner, M., Ciechanover, A., Fushman, D. & Brik, A. Oct 11 2013 In : Angewandte Chemie (International Edition in English). 52, 42, p. 11149-11153 5 p.

Research output: Research - peer-reviewArticle

Ubiquitin
Proteins
Organic Chemistry
Direction compound
14 Citations

Nonenzymatic assembly of branched polyubiquitin chains for structural and biochemical studies

Dixon, E. K., Castañeda, C. A., Kashyap, T. R., Wang, Y. & Fushman, D. Jun 15 2013 In : Bioorganic and Medicinal Chemistry. 21, 12, p. 3421-3429 9 p.

Research output: Research - peer-reviewArticle

Polyubiquitin
Ubiquitin
Ubiquitins
Lysine
Ubiquitin-Conjugating Enzymes
42 Citations

Recovering a representative conformational ensemble from underdetermined macromolecular structural data

Berlin, K., Castañeda, C. A., Schneidman-Duhovny, D., Sali, A., Nava-Tudela, A. & Fushman, D. Nov 6 2013 In : Journal of the American Chemical Society. 135, 44, p. 16595-16609 15 p.

Research output: Research - peer-reviewArticle

Conformations
Polyubiquitin
Entropy
Nucleic Acids
Proteins
31 Citations

Unique structural, dynamical, and functional properties of K11-linked polyubiquitin chains

Castañeda, C. A., Kashyap, T. R., Nakasone, M. A., Krueger, S. & Fushman, D. Jul 2 2013 In : Structure. 21, 7, p. 1168-1181 14 p.

Research output: Research - peer-reviewArticle

Polyubiquitin
Salts
Proteins
Ubiquitin
Eukaryota
2012
11 Citations

Evidence for cooperative and domain-specific binding of the signal transducing adaptor molecule 2 (STAM2) to Lys63-linked diubiquitin

Lange, A., Castañeda, C., Hoeller, D., Lancelin, J. M., Fushman, D. & Walker, O. May 25 2012 In : Journal of Biological Chemistry. 287, 22, p. 18687-18699 13 p.

Research output: Research - peer-reviewArticle

Ubiquitin
Molecules
Endosomal Sorting Complexes Required for Transport
Hepatocyte Growth Factor
Ports and harbors
2011
20 Citations

Controlled enzymatic synthesis of natural-linkage, defined-length polyubiquitin chains using lysines with removable protecting groups

Castañeda, C. A., Liu, J., Kashyap, T. R., Singh, R. K., Fushman, D. & Cropp, T. A. Feb 21 2011 In : Chemical Communications. 47, 7, p. 2026-2028 3 p.

Research output: Research - peer-reviewArticle

Polyubiquitin
Ubiquitin
Chain length
Lysine
Polymerization
135 Citations

Large shifts in pKa values of lysine residues buried inside a protein

Isom, D. G., Castañed, C. A., Cannon, B. R. & García-Moreno, B. E. Mar 29 2011 In : Proceedings of the National Academy of Sciences of the United States of America. 108, 13, p. 5260-5265 6 p.

Research output: Research - peer-reviewArticle

Lysine
Proteins
Catalysis
Micrococcal Nuclease
49 Citations

Nonenzymatic assembly of natural polyubiquitin chains of any linkage composition and isotopic labeling scheme

Castañeda, C., Liu, J., Chaturvedi, A., Nowicka, U., Cropp, T. A. & Fushman, D. Nov 9 2011 In : Journal of the American Chemical Society. 133, 44, p. 17855-17868 14 p.

Research output: Research - peer-reviewArticle

Labeling
Amines
Monomers
Chemical analysis
Polyubiquitin
16 Citations

Segmental isotopic labeling of ubiquitin chains to unravel monomer-specific molecular behavior

Castañeda, C. A., Spasser, L., Bavikar, S. N., Brik, A. & Fushman, D. Nov 18 2011 In : Angewandte Chemie (International Edition in English). 50, 47, p. 11210-11214 5 p.

Research output: Research - peer-reviewArticle

Ubiquitin
Labeling
Monomers
Ligands
Ubiquitins
23 Citations

Structural origins of high apparent dielectric constants experienced by ionizable groups in the hydrophobic core of a protein

García-Moreno, B., Chimenti, M. S., Castañeda, C. A. & Majumdar, A. Jan 14 2011 In : Journal of Molecular Biology. 405, 2, p. 361-377 17 p.

Research output: Research - peer-reviewArticle

Proteins
Micrococcal Nuclease
Static Electricity
Amides
Magnetic Resonance Spectroscopy
2010
96 Citations

Charges in the hydrophobic interior of proteins

Isom, D. G., Castañeda, C. A., Cannon, B. R., Velu, P. D. & García-Moreno E, B. Sep 14 2010 In : Proceedings of the National Academy of Sciences of the United States of America. 107, 37, p. 16096-16100 5 p.

Research output: Research - peer-reviewArticle

Proteins
Thermodynamics
Micrococcal Nuclease
Protein Stability
Circular Dichroism
8 Citations

Condensed E. coli cultures for highly efficient production of proteins containing unnatural amino acids

Liu, J., Castañeda, C. A., Wilkins, B. J., Fushman, D. & Cropp, T. A. Oct 1 2010 In : Bioorganic and Medicinal Chemistry Letters. 20, 19, p. 5613-5616 4 p.

Research output: Research - peer-reviewArticle

Escherichia coli
Amino Acids
Proteins
2009
93 Citations

Molecular determinants of the pK a values of Asp and Glu residues in staphylococcal nuclease

Castañeda, C. A., Fitch, C. A., Majumdar, A., Khangulov, V., Schlessman, J. L. & García-Moreno, B. E. Nov 15 2009 In : Proteins: Structure, Function and Genetics. 77, 3, p. 570-588 19 p.

Research output: Research - peer-reviewArticle

Micrococcal Nuclease
Viperidae
Static Electricity
Magnetic Resonance Spectroscopy
Acids
52 Citations

The pKa Values of Acidic and Basic Residues Buried at the Same Internal Location in a Protein Are Governed by Different Factors

Harms, M. J., Castañeda, C. A., Schlessman, J. L., Sue, G. R., Isom, D. G., Cannon, B. R. & García-Moreno E., B. May 29 2009 In : Journal of Molecular Biology. 389, 1, p. 34-47 14 p.

Research output: Research - peer-reviewArticle

Water
Proteins
Micrococcal Nuclease
Viperidae
Dehydration
2008
36 Citations

Direct evidence for deprotonation of a lysine side chain buried in the hydrophobic core of a protein

Takayama, Y., Castañeda, C. A., Chimenti, M., García-Moreno, B. & Iwahara, J. May 28 2008 In : Journal of the American Chemical Society. 130, 21, p. 6714-6715 2 p.

Research output: Research - peer-reviewArticle

Deprotonation
Chemical shift
Lysine
Amines
Hydrogen
87 Citations

High tolerance for ionizable residues in the hydrophobic interior of proteins

Isom, D. G., Cannon, B. R., Castañeda, C. A., Robinson, A. & García-Moreno E., B. Nov 18 2008 In : Proceedings of the National Academy of Sciences of the United States of America. 105, 46, p. 17784-17788 5 p.

Research output: Research - peer-reviewArticle

Proteins
Ribonuclease H
Micrococcal Nuclease
Protein Conformation
Viperidae
2004
72 Citations

Mapping and initial analysis of human subteloremeric sequence assemblies

Riethman, H., Ambrosini, A., Castaneda, C., Finklestein, J., Hu, X. L., Mudunuri, U., Paul, S. & Wei, J. Jan 2004 In : Genome Research. 14, 1, p. 18-28 11 p.

Research output: Research - peer-reviewArticle

DNA
Telomere
Genomic Segmental Duplications
Genome
Genes
2003
2 Citations

Human subtelomeric DNA

Riethman, H., Ambrosini, A., Castaneda, C., Finklestein, J. M., Hu, X. L., Paul, S. & Wei, J. 2003 In : Cold Spring Harbor Symposia on Quantitative Biology. 68, p. 39-47 9 p.

Research output: Research - peer-reviewArticle