Matthew Hj Cordes

  • 970 Citations
  • 18 h-Index
1985 …2019
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Research Output 1985 2019

  • 970 Citations
  • 18 h-Index
  • 43 Article
  • 1 Review article
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Article
2019
2 Citations (Scopus)

A shift in aggregation avoidance strategy marks a long-term direction to protein evolution

Foy, S. G., Wilson, B. A., Bertram, J., Cordes, M. H. & Masel, J., Apr 1 2019, In : Genetics. 211, 4, p. 1345-1355 11 p.

Research output: Contribution to journalArticle

Amino Acids
Genes
Proteins
Cluster Analysis
Poisons
Open Access
Bacteriophages
DNA
Binding Sites
Proteins
Protein Multimerization
2018
1 Citation (Scopus)

Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

Cordes, M. H. & Binford, G. J., Dec 18 2018, In : BMC Evolutionary Biology. 18, 1, 194.

Research output: Contribution to journalArticle

phospholipase D
toxin
toxins
gene transfer
history

Increased sequence hydrophobicity reduces conformational specificity: A mutational case study of the Arc repressor protein

Stewart, K. L., Rathore, D., Dodds, E. D. & Cordes, M. H., Jan 1 2018, (Accepted/In press) In : Proteins: Structure, Function and Bioinformatics.

Research output: Contribution to journalArticle

Repressor Proteins
Hydrophobicity
Hydrophobic and Hydrophilic Interactions
Substitution reactions
Mutation

Multistep mutational transformation of a protein fold through structural intermediates

Kumirov, V. K., Dykstra, E. M., Hall, B. M., Anderson, W. J., Szyszka, T. N. & Cordes, M. H., Oct 1 2018, In : Protein Science. 27, 10, p. 1767-1779 13 p.

Research output: Contribution to journalArticle

Proteins
Lizards
Plasticity
Switches
Nuclear magnetic resonance
3 Citations (Scopus)

Sexually dimorphic venom proteins in long-jawed orb-weaving spiders (Tetragnatha) comprise novel gene families

Zobel-Thropp, P. A., Bulger, E. A., Cordes, M. H., Binford, G. J., Gillespie, R. G. & Brewer, M. S., Jan 1 2018, In : PeerJ. 2018, 6, e4691.

Research output: Contribution to journalArticle

Tetragnathidae
Araneidae
Spiders
Venoms
venoms
2017
5 Citations (Scopus)

Foldability of a Natural De Novo Evolved Protein

Bungard, D., Copple, J. S., Yan, J., Chhun, J. J., Kumirov, V. K., Foy, S. G., Masel, J., Wysocki, V. H. & Cordes, M. H., 2017, (Accepted/In press) In : Structure.

Research output: Contribution to journalArticle

Proteins
DNA
Fungal Proteins
Amyloid
Libraries
2015
5 Citations (Scopus)

Spider, bacterial and fungal phospholipase D toxins make cyclic phosphate products

Lajoie, D. M. & Cordes, M. H., Dec 15 2015, In : Toxicon. 108, p. 176-180 5 p.

Research output: Contribution to journalArticle

Phospholipase D
Spiders
Phospholipids
Phosphates
Ascomycota
6 Citations (Scopus)

Studying protein fold evolution with hybrids of differently folded homologs

Eaton, K. V., Anderson, W. J., Dubrava, M. S., Kumirov, V. K., Dykstra, E. M. & Cordes, M. H., 2015, In : Protein Engineering, Design and Selection. 28, 8, p. 241-250 10 p.

Research output: Contribution to journalArticle

Proteins
Thermodynamic stability
Substitution reactions
Hot Temperature
5-oxo-5H-benzo(e)isochromeno(4,3-b)indole
8 Citations (Scopus)

The recent de Novo origin of protein C-termini

Andreatta, M. E., Levine, J. A., Foy, S. G., Guzman, L. D., Kosinski, L. J., Cordes, M. H. & Masel, J., 2015, In : Genome Biology and Evolution. 7, 6, p. 1686-1701 16 p.

Research output: Contribution to journalArticle

Protein C
Saccharomyces
protein
gene
Proteins
13 Citations (Scopus)

Variable substrate preference among phospholipase D toxins from sicariid spiders

Lajoie, D. M., Roberts, S. A., Zobel-Thropp, P. A., Delahaye, J. L., Bandarian, V., Binford, G. J. & Cordes, M. H., Apr 24 2015, In : Journal of Biological Chemistry. 290, 17, p. 10994-11007 14 p.

Research output: Contribution to journalArticle

Phospholipase D
Sphingolipids
Spiders
Choline
Ethanolamine
2013
5 Citations (Scopus)

A polymetamorphic protein

Stewart, K. L., Dodds, E. D., Wysocki, V. H. & Cordes, M. H., May 2013, In : Protein Science. 22, 5, p. 641-649 9 p.

Research output: Contribution to journalArticle

Amyloid
Topology
Oligomerization
Mutation
Proteins
4 Citations (Scopus)

A role for indels in the evolution of Cro protein folds

Stewart, K. L., Nelson, M. R., Eaton, K. V., Anderson, W. J. & Cordes, M. H., Nov 2013, In : Proteins: Structure, Function and Genetics. 81, 11, p. 1988-1996 9 p.

Research output: Contribution to journalArticle

Proteins
Sequence Alignment
INDEL Mutation
Protein Unfolding
Alternative Splicing
20 Citations (Scopus)

Phospholipase D Toxins of Brown Spider Venom Convert Lysophosphatidylcholine and Sphingomyelin to Cyclic Phosphates

Lajoie, D. M., Zobel-Thropp, P. A., Kumirov, V. K., Bandarian, V., Binford, G. J. & Cordes, M. H., Aug 29 2013, In : PLoS One. 8, 8, e72372.

Research output: Contribution to journalArticle

Spider Venoms
lysophosphatidylcholine
Phospholipase D
phospholipase D
sphingomyelins
2012
5 Citations (Scopus)

The porous borders of the protein world

Cordes, M. H. & Stewart, K. L., Feb 8 2012, In : Structure. 20, 2, p. 199-200 2 p.

Research output: Contribution to journalArticle

Proteins
2011
24 Citations (Scopus)

Determinants of gas-phase disassembly behavior in homodimeric protein complexes with related yet divergent structures

Dodds, E. D., Blackwell, A. E., Jones, C. M., Holso, K. L., O'Brien, D. J., Cordes, M. H. & Wysocki, V. H., May 15 2011, In : Analytical Chemistry. 83, 10, p. 3881-3889 9 p.

Research output: Contribution to journalArticle

Gases
Proteins
Bacteriophages
Dimers
Mass spectrometry
12 Citations (Scopus)

Evolutionary bridges to new protein folds: Design of C-terminal Cro protein chameleon sequences

Anderson, W. J., Van Dorn, L. O., Ingram, W. M. & Cordes, M. H., Sep 2011, In : Protein Engineering, Design and Selection. 24, 9, p. 765-771 7 p.

Research output: Contribution to journalArticle

Lizards
Conformations
Proteins
Denaturation
Transcription factors
11 Citations (Scopus)

Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy

Bouvignies, G., Vallurupalli, P., Cordes, M. H., Hansen, D. F. & Kay, L. E., May 2011, In : Journal of Biomolecular NMR. 50, 1, p. 13-18 6 p.

Research output: Contribution to journalArticle

Amides
Nuclear magnetic resonance spectroscopy
Magnetic Resonance Spectroscopy
Protein Unfolding
Temperature
3 Citations (Scopus)

Reengineering Cro protein functional specificity with an evolutionary code

Hall, B. M., Vaughn, E. E., Begaye, A. R. & Cordes, M. H., Nov 11 2011, In : Journal of Molecular Biology. 413, 5, p. 914-928 15 p.

Research output: Contribution to journalArticle

Bacteriophages
Proteins
Fluorescence Polarization
DNA
Consensus Sequence
2010
18 Citations (Scopus)

A simple method for measuring signs of 1HN chemical shift differences between ground and excited protein states

Bouvignies, G., Korzhnev, D. M., Neudecker, P., Hansen, D. F., Cordes, M. H. & Kay, L. E., Jun 2010, In : Journal of Biomolecular NMR. 47, 2, p. 135-141 7 p.

Research output: Contribution to journalArticle

Chemical shift
Excited states
Structural analysis
Ion exchange
Proteins
2009
72 Citations (Scopus)

Molecular evolution, functional variation, and proposed nomenclature of the gene family that includes sphingomyelinase D in sicariid spider venoms

Binford, G. J., Bodner, M. R., Cordes, M. H., Baldwin, K. L., Rynerson, M. R., Burns, S. N. & Zobel-Thropp, P. A., Mar 2009, In : Molecular Biology and Evolution. 26, 3, p. 547-566 20 p.

Research output: Contribution to journalArticle

Loxosceles
Spider Venoms
venom
Molecular Evolution
venoms
2008
10 Citations (Scopus)

N15 Cro and λ Cro: Orthologous DNA-binding domains with completely different but equally effective homodimer interfaces

Dubrava, M. S., Ingram, W. M., Roberts, S. A., Weichsel, A., Montfort, W. B. & Cordes, M. H., May 2008, In : Protein Science. 17, 5, p. 803-812 10 p.

Research output: Contribution to journalArticle

Dimerization
Dimers
Bacteriophages
DNA
Enterobacteriaceae
20 Citations (Scopus)

Structural features and the persistence of acquired proteins

Narra, H. P., Cordes, M. H. & Ochman, H., Nov 2008, In : Proteomics. 8, 22, p. 4772-4781 10 p.

Research output: Contribution to journalArticle

Genes
Proteins
Escherichia coli
Bacterial Genomes
Circular Dichroism
66 Citations (Scopus)
Proteins
Bacteriophage P22
Dimerization
Bacteriophages
Amino Acid Sequence
10 Citations (Scopus)
DNA
Proteins
Mutation
2007
12 Citations (Scopus)

Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage λ

Degnan, P. H., Michalowski, C. B., Babić, A. C., Cordes, M. H. & Little, J. W., Apr 2007, In : Molecular Microbiology. 64, 1, p. 232-244 13 p.

Research output: Contribution to journalArticle

Bacteriophages
Immunity
Mosaicism
Lysogeny
Nucleic Acid Regulatory Sequences
2006
10 Citations (Scopus)

A trade between similar but nonequivalent intrasubunit and intersubunit contacts in Cro dimer evolution

Newlove, T., Atkinson, K. R., Van Dorn, L. O. & Cordes, M. H., May 23 2006, In : Biochemistry. 45, 20, p. 6379-6391 13 p.

Research output: Contribution to journalArticle

Dimers
Monomers
Dimerization
Tryptophan
Mutation
9 Citations (Scopus)
Proteins
Amino Acids
Amyloid
Aspartic Acid
Alzheimer Disease
24 Citations (Scopus)

Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria

Cordes, M. H. & Binford, G. J., Feb 1 2006, In : Bioinformatics. 22, 3, p. 264-268 5 p.

Research output: Contribution to journalArticle

Gene transfer
Horizontal Gene Transfer
Spiders
Poisons
Bacteria
22 Citations (Scopus)

Relationship between sequence determinants of stability for two natural homologous proteins with different folds

Van Dorn, L. O., Newlove, T., Chang, S., Ingram, W. M. & Cordes, M. H., Sep 5 2006, In : Biochemistry. 45, 35, p. 10542-10553 12 p.

Research output: Contribution to journalArticle

Proteins
Protein C
Scanning
Mutagenesis
Nuclear magnetic resonance
2005

Networking at the Protein Society symposium.

McKnight, C. J. & Cordes, M. H., Oct 2005, In : Nature Chemical Biology. 1, 5, p. 239-242 4 p.

Research output: Contribution to journalArticle

Systems Biology
Proteins
Protein Aggregates
11 Citations (Scopus)

Sequence correlations between Cro recognition helices and cognate O R consensus half-sites suggest conserved rules of protein-DNA pecognition

Hall, B. M., LeFevre, K. R. & Cordes, M. H., Jul 22 2005, In : Journal of Molecular Biology. 350, 4, p. 667-681 15 p.

Research output: Contribution to journalArticle

Amino Acids
DNA
Proteins
Bacteriophages
Sequence Alignment
24 Citations (Scopus)

Sequence determinants of a conformational switch in a protein structure

Anderson, T. A., Cordes, M. H. & Sauer, R. T., Dec 20 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 51, p. 18344-18349 6 p.

Research output: Contribution to journalArticle

Bacteriophage P22
Mutation
Proteins
Transcription Factors
44 Citations (Scopus)

Sphingomyelinase D from venoms of Loxosceles spiders: Evolutionary insights from cDNA sequences and gene structure

Binford, G. J., Cordes, M. H. & Wells, M. A., Apr 2005, In : Toxicon. 45, 5, p. 547-560 14 p.

Research output: Contribution to journalArticle

Spider Venoms
Complementary DNA
Genes
Spiders
Bacteria
2004
33 Citations (Scopus)

Secondary structure switching in Cro protein evolution

Newlove, T., Konieczka, J. H. & Cordes, M. H., Apr 2004, In : Structure. 12, 4, p. 569-581 13 p.

Research output: Contribution to journalArticle

Bacteriophage P22
Proteins
2003
38 Citations (Scopus)

Retroevolution of λ Cro toward a stable monomer

LeFevre, K. R. & Cordes, M. H., Mar 4 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 5, p. 2345-2350 6 p.

Research output: Contribution to journalArticle

Dimerization
Mutation
Sequence Alignment
Tertiary Protein Structure
Tryptophan
13 Citations (Scopus)

Solution structure of switch Arc, a mutant with 310 helices replacing a wild-type β-ribbon

Cordes, M. H., Walsh, N. P., McKnight, C. J. & Sauer, R. T., Feb 21 2003, In : Journal of Molecular Biology. 326, 3, p. 899-909 11 p.

Research output: Contribution to journalArticle

Hydrogen
Static Electricity
Amino Acid Sequence
Proteins
Salts
2000
73 Citations (Scopus)

An evolutionary bridge to a new protein fold

Cordes, M. H., Burton, R. E., Walsh, N. P., McKnight, C. J. & Sauer, R. T., 2000, In : Nature Structural Biology. 7, 12, p. 1129-1132 4 p.

Research output: Contribution to journalArticle

Bearings (structural)
Conformations
Substitution reactions
Switches
Ligands
1999
46 Citations (Scopus)

Tolerance of a protein to multiple polar-to-hydrophobic surface substitutions

Cordes, M. H. & Sauer, R. T., 1999, In : Protein Science. 8, 2, p. 318-325 8 p.

Research output: Contribution to journalArticle

Bacteriophage P22
Mutagenesis
Substitution reactions
Hot Temperature
Proteins
1996
18 Citations (Scopus)
Ground state
Stabilization
Ether
Ethers
Heptane
135 Citations (Scopus)

Sequence space, folding and protein design

Cordes, M. H., Davidson, A. R. & Sauer, R. T., Feb 1996, In : Current Opinion in Structural Biology. 6, 1, p. 3-10 8 p.

Research output: Contribution to journalArticle

Protein Folding
Protein Stability
Proteins
Peptides
1994
23 Citations (Scopus)
Stereochemistry
Ether
Ethers
Crystal structure
cyclopropenone
1985
86 Citations (Scopus)
alanylproline
Peptidyl-Dipeptidase A
Proline
Rate constants
Rabbits