Works by Harms, Michael J.

Results: 26

Thermodynamic System Drift in Protein Evolution.

Published in:

PLoS Biology, 2014, v. 12, n. 11, p. 1, doi. 10.1371/journal.pbio.1001994

By:

Hart, Kathryn M.;
Harms, Michael J.;
Schmidt, Bryan H.;
Elya, Carolyn;
Thornton, Joseph W.;
Marqusee, Susan

Publication type:

Article

Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand- Dependent Ancestor.

Published in:

PLoS Biology, 2010, v. 8, n. 10, p. 1, doi. 10.1371/journal.pbio.1000497

By:

Bridgham, Jamie T.;
Eick, Geeta N.;
Larroux, Claire;
Deshpande, Kirti;
Harms, Michael J.;
Gauthier, Marie E. A.;
Ortlund, Eric A.;
Degnan, Bernard M.;
Thornton, Joseph W.

Publication type:

Article

Bacterial vampirism mediated through taxis to serum.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.93178

By:

Glenn, Siena J.;
Gentry-Lear, Zealon;
Shavlik, Michael;
Harms, Michael J.;
Asaki, Thomas J.;
Baylink, Arden

Publication type:

Article

Structural Deformations in Cucurbit[n]urils: Analysis, Host‐Guest Dependence, and Automated Ellipticity Measurements Using ElliptiCB[n].

Published in:

Chemistry - A European Journal, 2024, v. 30, n. 57, p. 1, doi. 10.1002/chem.202401981

By:

Garcia, Arman C.;
Shavlik, Michael;
Harms, Michael J.;
Pluth, Michael D.

Publication type:

Article

Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors.

Published in:

PLoS Genetics, 2012, v. 8, n. 11, p. 1, doi. 10.1371/journal.pgen.1003072

By:

Eick, Geeta N.;
Colucci, Jennifer K.;
Harms, Michael J.;
Ortlund, Eric A.;
Thornton, Joseph W.

Publication type:

Article

High-order epistasis shapes evolutionary trajectories.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 5, p. 1, doi. 10.1371/journal.pcbi.1005541

By:

Sailer, Zachary R.;
Harms, Michael J.

Publication type:

Article

Higher-order interactions shape microbial interactions as microbial community complexity increases.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-25303-1

By:

Morin, Manon A.;
Morrison, Anneliese J.;
Harms, Michael J.;
Dutton, Rachel J.

Publication type:

Article

Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide.

Published in:

Frontiers in Immunology, 2018, p. 1, doi. 10.3389/fimmu.2018.00304

By:

Loes, Andrea N.;
Bridgham, Jamie T.;
Harms, Michael J.

Publication type:

Article

Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family.

Published in:

PLoS ONE, 2016, v. 11, n. 10, p. 1, doi. 10.1371/journal.pone.0164740

By:

Wheeler, Lucas C.;
Donor, Micah T.;
Prell, James S.;
Harms, Michael J.

Publication type:

Article

Evolutionary biochemistry: revealing the historical and physical causes of protein properties.

Published in:

Nature Reviews Genetics, 2013, v. 14, n. 8, p. 559, doi. 10.1038/nrg3540

By:

Harms, Michael J.;
Thornton, Joseph W.

Publication type:

Article

The importance of input sequence set to consensus‐derived proteins and their relationship to reconstructed ancestral proteins.

Published in:

Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 6, p. 1, doi. 10.1002/pro.5011

By:

Nixon, Charlotte;
Lim, Shion A.;
Sternke, Matt;
Barrick, Doug;
Harms, Michael J.;
Marqusee, Susan

Publication type:

Article

Topiary: Pruning the manual labor from ancestral sequence reconstruction.

Published in:

Protein Science: A Publication of the Protein Society, 2023, v. 32, n. 2, p. 1, doi. 10.1002/pro.4551

By:

Orlandi, Kona N.;
Phillips, Sophia R.;
Sailer, Zachary R.;
Harman, Joseph L.;
Harms, Michael J.

Publication type:

Article

Probing the origin of prion protein misfolding via reconstruction of ancestral proteins.

Published in:

Protein Science: A Publication of the Protein Society, 2022, v. 31, n. 12, p. 1, doi. 10.1002/pro.4477

By:

Cortez, Leonardo M.;
Morrison, Anneliese J.;
Garen, Craig R.;
Patterson, Sawyer;
Uyesugi, Toshi;
Petrosyan, Rafayel;
Sekar, Rohith Vedhthaanth;
Harms, Michael J.;
Woodside, Michael T.;
Sim, Valerie L.

Publication type:

Article

Learning peptide recognition rules for a low‐specificity protein.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 11, p. 2259, doi. 10.1002/pro.3958

By:

Wheeler, Lucas C.;
Perkins, Arden;
Wong, Caitlyn E.;
Harms, Michael J.

Publication type:

Article

Tracing the evolution of novel features of human Toll‐like receptor 4.

Published in:

Protein Science: A Publication of the Protein Society, 2019, v. 28, n. 7, p. 1350, doi. 10.1002/pro.3644

By:

Anderson, Jeremy A.;
Loes, Andrea N.;
Waddell, Grace L.;
Harms, Michael J.

Publication type:

Article

A buried lysine that titrates with a normal p Ka: Role of conformational flexibility at the protein-water interface as a determinant of p Kavalues.

Published in:

Protein Science: A Publication of the Protein Society, 2008, v. 17, n. 5, p. 833, doi. 10.1110/ps.073397708

By:

Harms, Michael J.;
Schlessman, Jamie L.;
Chimenti, Michael S.;
Sue, Gloria R.;
Damjanović, Ana;
García-Moreno E., Bertrand

Publication type:

Article

Laser light-scattering evidence for an altered association of βB1-crystallin deamidated in the connecting peptide.

Published in:

Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 3, p. 678, doi. 10.1110/ps.03427504

By:

Harms, Michael J.;
Wilmarth, Philip A.;
Kapfer, Deborah M.;
Steel, Eric A.;
David, Larry L.;
Bächinger, Hans Peter;
Lampi, Kirsten J.

Publication type:

Article

Were Ancestral Proteins Less Specific?

Published in:

Molecular Biology & Evolution, 2021, v. 38, n. 6, p. 2227, doi. 10.1093/molbev/msab019

By:

Wheeler, Lucas C;
Harms, Michael J

Publication type:

Article

Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 2, p. 247, doi. 10.1093/molbev/msw223

By:

Eick, Geeta N.;
Bridgham, Jamie T.;
Anderson, Douglas P.;
Harms, Michael J.;
Thornton, Joseph W.

Publication type:

Article

Zebrafish do not have a calprotectin ortholog.

Published in:

PLoS ONE, 2025, v. 20, n. 5, p. 1, doi. 10.1371/journal.pone.0322649

By:

Orlandi, Kona N.;
Harms, Michael J.

Publication type:

Article

Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities.

Published in:

Bacteria (2674-1334), 2022, v. 1, n. 2, p. 121, doi. 10.3390/bacteria1020011

By:

Valgardson, Jordan D.;
Struyvenberg, Sarah A.;
Sailer, Zachary R.;
Piper, Isabel M.;
Svendsen, Justin E.;
Johnson, D. Alex;
Vogel, Brandon A.;
Antos, John M.;
Harms, Michael J.;
Amacher, Jeanine F.

Publication type:

Article

Human S100A5 binds Ca2+ and Cu2+ independently.

Published in:

BMC Biophysics, 2017, v. 10, p. 1, doi. 10.1186/s13628-017-0040-y

By:

Wheeler, Lucas C.;
Harms, Michael J.

Publication type:

Article

Inferring a complete genotype-phenotype map from a small number of measured phenotypes.

Published in:

PLoS Computational Biology, 2020, v. 16, n. 9, p. 1, doi. 10.1371/journal.pcbi.1008243

By:

Sailer, Zachary R.;
Shafik, Sarah H.;
Summers, Robert L.;
Joule, Alex;
Patterson-Robert, Alice;
Martin, Rowena E.;
Harms, Michael J.

Publication type:

Article

Ensemble epistasis: thermodynamic origins of nonadditivity between mutations.

Published in:

Genetics, 2021, v. 219, n. 1, p. 1, doi. 10.1093/genetics/iyab105

By:

Morrison, Anneliese J.;
Wonderlick, Daria R.;
Harms, Michael J.

Publication type:

Article

Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps.

Published in:

Genetics, 2017, v. 205, n. 3, p. 1079, doi. 10.1534/genetics.116.195214

By:

Sailer, Zachary R.;
Harms, Michael J.

Publication type:

Article

Historical contingency and its biophysical basis in glucocorticoid receptor evolution.

Published in:

Nature, 2014, v. 512, n. 7513, p. 203, doi. 10.1038/nature13410

By:

Harms, Michael J.;
Thornton, Joseph W.

Publication type:

Article

Works by Harms, Michael J.

Thermodynamic System Drift in Protein Evolution.

Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand- Dependent Ancestor.

Bacterial vampirism mediated through taxis to serum.

Structural Deformations in Cucurbit[n]urils: Analysis, Host‐Guest Dependence, and Automated Ellipticity Measurements Using ElliptiCB[n].

Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors.

High-order epistasis shapes evolutionary trajectories.

Higher-order interactions shape microbial interactions as microbial community complexity increases.

Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide.

Multiple Evolutionary Origins of Ubiquitous Cu<sup>2+</sup> and Zn<sup>2+</sup> Binding in the S100 Protein Family.

Evolutionary biochemistry: revealing the historical and physical causes of protein properties.

The importance of input sequence set to consensus‐derived proteins and their relationship to reconstructed ancestral proteins.

Topiary: Pruning the manual labor from ancestral sequence reconstruction.

Probing the origin of prion protein misfolding via reconstruction of ancestral proteins.

Learning peptide recognition rules for a low‐specificity protein.

Tracing the evolution of novel features of human Toll‐like receptor 4.

A buried lysine that titrates with a normal p K<sub>a</sub>: Role of conformational flexibility at the protein-water interface as a determinant of p K<sub>a</sub>values.

Laser light-scattering evidence for an altered association of βB1-crystallin deamidated in the connecting peptide.

Were Ancestral Proteins Less Specific?

Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty.

Zebrafish do not have a calprotectin ortholog.

Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities.

Human S100A5 binds Ca<sup>2+</sup> and Cu<sup>2+</sup> independently.

Inferring a complete genotype-phenotype map from a small number of measured phenotypes.

Ensemble epistasis: thermodynamic origins of nonadditivity between mutations.

Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps.

Historical contingency and its biophysical basis in glucocorticoid receptor evolution.